Contacts of the helix formed by residues 300 - 325 (chain A) in PDB entry 2XXA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 3.9 25.1 - - + +
75A VAL* 4.8 14.4 - - + -
297A MET* 4.2 28.7 - - + +
298A GLY* 3.2 0.4 - - - -
299A ASP* 1.3 80.0 - - + +
301A LEU* 1.4 63.0 + - - +
303A LEU* 3.3 7.2 + - - +
304A ILE* 3.2 42.1 + - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 4.1 26.2 - - + -
76A LYS* 5.4 3.6 - - + +
79A ARG* 3.8 38.4 - - + +
292A SER* 5.1 9.6 - - - +
295A LEU* 3.9 27.6 - - + -
297A MET* 3.5 19.7 + - + +
298A GLY* 3.5 10.3 + - - +
300A VAL* 1.4 74.8 - - - +
302A SER* 1.4 63.2 + - - +
303A LEU 3.3 0.2 - - - -
304A ILE* 4.1 13.1 - - + +
305A GLU* 3.2 39.8 + - + +
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLY 2.8 17.3 + - - -
299A ASP* 3.0 23.0 + - - -
301A LEU* 1.4 75.2 - - - +
303A LEU* 1.4 60.0 + - - +
305A GLU* 4.3 4.8 - - - +
306A ASP* 3.3 25.6 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLN* 5.9 2.5 - - - +
299A ASP 3.9 13.9 - - - +
300A VAL* 3.3 9.5 + - - +
301A LEU 3.3 0.4 - - - -
302A SER* 1.4 81.4 + - - +
304A ILE* 1.4 55.8 + - + +
305A GLU 3.3 0.4 - - - -
306A ASP* 3.1 7.8 + - + +
307A ILE* 2.7 64.9 + - + +
310A LYS* 5.7 5.2 - - - +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.9 34.4 - - + +
72A GLN* 3.4 29.4 - - + +
75A VAL* 4.3 12.3 - - + -
76A LYS* 3.9 18.2 - - + -
300A VAL* 3.2 38.4 + - + +
301A LEU* 3.6 13.7 + - + +
303A LEU* 1.4 74.1 - - + +
305A GLU* 1.4 59.2 + - + +
307A ILE* 4.0 1.0 - - - +
308A GLU* 3.1 52.7 + - + +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 2.9 45.8 + - - +
301A LEU* 3.2 29.4 + - + +
302A SER* 4.5 4.8 - - - +
304A ILE* 1.4 77.0 - - + +
306A ASP* 1.4 56.1 + - - +
308A GLU* 4.3 11.7 - - - +
309A SER* 3.2 22.7 + - - -
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Residues in contact with ASP 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A SER 3.3 20.1 + - - +
303A LEU* 3.1 12.9 + - + +
305A GLU* 1.4 76.0 - - - +
307A ILE* 1.4 62.9 + - + +
309A SER* 2.7 22.3 + - - -
310A LYS* 3.3 40.4 + - - +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 5.1 7.9 - - - +
68A LEU* 3.8 31.0 - - + -
72A GLN* 5.2 4.9 - - - +
303A LEU* 2.7 51.3 + - + +
304A ILE 4.1 3.1 - - - +
306A ASP* 1.4 70.0 - - - +
308A GLU* 1.4 64.7 + - + +
310A LYS* 3.2 18.5 + - + +
311A VAL* 3.2 32.6 + - + +
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 5.9 3.1 - - + -
76A LYS* 3.5 28.3 + - - +
304A ILE* 3.1 39.3 + - + +
305A GLU* 4.4 11.9 + - - +
307A ILE* 1.4 77.5 - - + +
309A SER* 1.4 50.8 + - - +
311A VAL* 3.3 8.0 + - - +
312A ASP* 2.8 47.8 + - - +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLU 3.2 16.5 + - - -
306A ASP* 2.7 28.2 + - - -
308A GLU* 1.4 75.3 - - - +
310A LYS* 1.4 60.0 + - - +
312A ASP* 3.8 9.4 - - - +
313A ARG* 3.0 39.8 + - - +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 5.7 4.8 - - - +
306A ASP* 3.3 34.2 + - - +
307A ILE* 3.2 23.1 + - + +
309A SER* 1.4 80.3 + - - +
311A VAL* 1.4 61.5 + - + +
313A ARG* 3.4 48.6 + - - +
314A ALA* 3.4 13.5 - - - +
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 5.1 12.6 - - - +
307A ILE* 3.2 25.2 + - + +
308A GLU* 3.6 9.6 - - - +
310A LYS* 1.4 76.6 - - + +
312A ASP* 1.4 55.0 + - - +
314A ALA* 3.2 5.6 + - - +
315A GLN* 2.8 64.8 + - + +
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Residues in contact with ASP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 2.8 38.1 + - - +
309A SER* 3.8 9.8 + - - +
311A VAL* 1.4 73.0 - - - +
313A ARG* 1.4 59.4 + - - +
315A GLN* 3.8 14.1 + - - +
316A ALA* 3.4 23.7 + - - +
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Residues in contact with ARG 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER* 3.0 25.3 + - - +
310A LYS* 3.4 44.2 + - - +
312A ASP* 1.4 74.5 - - - +
314A ALA* 1.4 62.0 + - + +
316A ALA* 3.6 3.6 + - - +
317A GLU* 3.0 49.8 + - - +
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LYS 3.4 16.8 + - - +
311A VAL* 3.2 7.1 + - - +
313A ARG* 1.4 79.9 - - + +
315A GLN* 1.4 59.1 + - + +
317A GLU* 4.2 5.5 - - - +
318A LYS* 3.2 47.2 + - - +
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Residues in contact with GLN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 2.8 44.2 + - + +
312A ASP* 4.0 15.8 - - - +
314A ALA* 1.4 74.7 - - + +
316A ALA* 1.4 57.5 + - - +
318A LYS* 4.7 2.9 - - - +
319A LEU* 3.3 28.6 + - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ASP 3.4 16.2 + - - +
313A ARG* 3.9 6.1 - - - +
314A ALA 3.3 0.4 - - - -
315A GLN* 1.4 78.5 - - - +
317A GLU* 1.4 60.0 + - + +
318A LYS 3.5 0.2 - - - -
319A LEU* 3.6 4.7 + - - +
320A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ARG* 3.0 40.6 + - - +
314A ALA* 4.2 5.4 - - - +
315A GLN 3.6 0.2 - - - -
316A ALA* 1.4 78.2 - - + +
318A LYS* 1.4 62.2 + - + +
320A ALA* 3.6 5.8 + - - +
321A SER* 3.5 22.7 + - - -
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA* 3.2 29.7 + - + +
315A GLN* 4.7 3.1 - - - +
317A GLU* 1.4 75.0 - - + +
319A LEU* 1.4 56.7 + - - +
321A SER* 3.2 17.2 + - - -
322A LYS* 3.4 24.5 - - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLN 3.3 19.9 + - - +
316A ALA* 3.6 6.0 + - - +
317A GLU 3.3 0.6 - - - -
318A LYS* 1.4 77.8 - - - +
320A ALA* 1.4 56.8 + - - +
321A SER 3.4 0.7 - - - -
322A LYS* 3.4 12.3 + - + +
323A LEU* 3.0 54.2 + - + +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA 3.0 19.7 + - - +
317A GLU* 3.9 7.4 - - - +
319A LEU* 1.4 76.6 - - - +
321A SER* 1.4 57.9 + - - +
323A LEU* 3.4 10.4 + - - +
324A LYS* 3.0 48.5 + - - +
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLU 3.5 11.7 + - - -
318A LYS* 3.2 17.3 + - - -
320A ALA* 1.4 76.7 - - - +
322A LYS* 1.3 62.3 + - - +
324A LYS* 3.5 8.1 + - - +
325A LYS* 3.1 48.2 + - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 3.4 19.5 - - - +
319A LEU* 3.4 17.6 + - + +
320A ALA 3.3 0.4 - - - -
321A SER* 1.3 82.4 + - - +
323A LEU* 1.4 59.1 + - + +
325A LYS* 3.6 5.1 + - - +
326A GLY* 3.2 23.7 + - - -
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.0 44.6 + - + +
320A ALA* 3.8 8.3 - - - +
321A SER 3.4 0.2 - - - -
322A LYS* 1.4 75.3 - - + +
324A LYS* 1.3 61.8 + - + +
325A LYS 3.5 0.2 - - - -
326A GLY* 3.7 9.6 + - - -
327A ASP* 5.2 1.0 - - - +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ALA* 3.0 33.5 + - - +
321A SER* 3.8 7.6 - - - +
322A LYS 3.3 0.2 - - - -
323A LEU* 1.3 77.7 - - + +
325A LYS* 1.4 57.0 + - + +
326A GLY 3.2 2.2 - - - -
327A ASP* 3.0 23.4 - - - +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A SER* 3.1 30.4 + - - +
322A LYS* 3.7 6.3 - - - +
323A LEU 3.5 0.2 - - - -
324A LYS* 1.4 75.5 - - + +
326A GLY* 1.3 56.3 + - - +
327A ASP* 3.2 10.1 + - - -
328A GLY* 3.6 12.1 + - - -
330A ASP* 4.4 22.4 - - - +
332A ASN* 4.8 13.4 + - + +
333A ASP* 5.4 2.1 - - - +
389A ALA* 5.3 11.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il