Contacts of the helix formed by residues 300 - 318 (chain A) in PDB entry 4O5A
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 ASN 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A SER 4.1 1.4 + - - -
299A ARG* 1.3 70.8 - - - +
301A ILE* 1.3 56.0 + - - +
302A LEU* 3.8 6.8 + - - +
303A GLU* 3.1 34.6 + - - +
304A SER* 3.0 30.7 + - - -
326A GLU* 5.0 2.8 + - - -
327A PRO* 4.1 20.1 + - + +
328A PRO* 4.2 15.4 + - - +
329A TYR* 5.0 0.2 - - - +
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.5 50.5 - - + +
87A ARG* 3.4 40.2 - - + +
88A LEU* 3.5 32.3 - - + +
299A ARG* 3.0 26.2 + - + +
300A ASN* 1.3 70.5 + - - +
302A LEU* 1.3 65.9 + - - +
304A SER* 3.4 6.7 - - - -
305A GLY* 2.9 21.1 + - - -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.4 33.7 - - + +
90A SER* 3.8 12.6 - - - -
91A GLY* 3.3 23.3 - - - +
300A ASN* 3.4 7.5 + - - +
301A ILE* 1.3 77.7 - - - +
303A GLU* 1.3 62.6 + - - +
305A GLY 3.1 2.8 + - - -
306A ARG* 3.0 19.8 + - - +
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Residues in contact with GLU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ASN* 3.1 30.6 + - - +
302A LEU* 1.3 75.9 - - - +
304A SER* 1.3 60.8 + - - +
306A ARG* 3.8 22.0 - - - +
307A LEU* 2.9 37.3 + - + +
310A GLN* 4.8 2.1 - - - +
327A PRO* 3.5 21.5 - - + +
404A SO4 3.6 18.1 + - - -
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Residues in contact with SER 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.3 9.2 - - - -
156A LEU* 5.3 1.8 - - - -
168A LEU* 3.3 19.3 - - - +
299A ARG* 4.4 8.6 + - - -
300A ASN 3.0 21.1 + - - -
301A ILE* 3.4 10.4 - - - -
302A LEU 3.2 0.2 - - - -
303A GLU* 1.3 76.4 - - - +
305A GLY* 1.3 58.6 + - - +
307A LEU* 3.3 0.9 + - - -
308A ALA* 2.9 26.2 + - - +
326A GLU* 3.9 18.3 + - - +
327A PRO* 3.4 22.6 - - - +
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Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.6 34.0 - - - +
92A LEU* 3.4 21.2 - - - +
301A ILE 2.9 11.8 + - - -
302A LEU 3.6 3.4 - - - -
304A SER* 1.3 78.0 - - - +
306A ARG* 1.3 61.2 + - - +
308A ALA* 3.3 2.8 + - - -
309A ALA 3.1 18.4 + - - -
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY* 3.3 13.8 + - - +
94A SER* 3.2 36.1 + - - +
95A ALA* 3.7 9.4 - - + +
98A GLU* 2.7 33.5 + - - -
302A LEU 3.0 11.5 + - - +
303A GLU* 3.6 22.4 - - - +
305A GLY* 1.3 77.2 - - - +
307A LEU* 1.3 62.9 + - - +
309A ALA 3.4 1.2 + - - -
310A GLN* 3.1 40.0 + - - +
404A SO4 2.9 42.9 + - - +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.7 19.1 - - + -
303A GLU* 2.9 24.8 + - + +
304A SER* 3.7 4.3 - - - +
306A ARG* 1.3 76.3 - - - +
308A ALA* 1.3 58.0 - - - +
310A GLN* 3.2 20.3 + - + +
311A LEU* 2.9 49.7 + - + +
324A VAL* 3.6 28.0 - - + -
325A GLU 4.0 6.1 - - - +
327A PRO* 4.4 12.3 - - + -
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 5.7 0.4 - - + -
92A LEU* 4.1 10.5 - - + -
131A LEU* 4.5 4.3 - - + -
154A LEU* 3.5 30.4 - - + +
156A LEU* 4.1 12.3 - - + -
168A LEU* 4.0 10.5 - - + +
304A SER 2.9 17.2 + - - +
305A GLY* 3.5 8.5 - - - +
306A ARG 3.2 0.2 - - - -
307A LEU* 1.3 77.2 - - - +
309A ALA* 1.3 61.7 + - - +
311A LEU* 3.3 1.3 + - - -
312A MSE 3.0 24.5 + - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.6 30.7 - - + +
95A ALA* 3.7 14.8 - - + -
96A LEU* 3.8 16.9 - - + +
305A GLY 3.1 10.7 + - - +
306A ARG 3.7 1.8 - - - +
308A ALA* 1.3 73.0 - - - +
310A GLN* 1.3 65.2 + - - +
312A MSE 3.3 13.5 + - - +
313A LEU* 2.9 30.1 + - - +
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Residues in contact with GLN 310 (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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95A ALA* 4.0 11.8 - - + +
98A GLU* 5.0 2.0 + - - -
303A GLU* 4.8 1.2 - - - +
306A ARG* 3.1 34.9 + - - +
307A LEU* 3.6 29.4 - - + +
309A ALA* 1.3 75.8 - - - +
311A LEU* 1.3 63.6 + - + +
313A LEU* 3.4 10.6 + - + +
314A LYS* 3.0 33.8 + - - +
404A SO4 3.1 34.3 + - - -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.2 27.8 - - + -
167A THR 5.2 0.7 - - - +
168A LEU* 4.2 11.2 - - + -
307A LEU* 2.9 37.8 + - + +
308A ALA 3.7 4.3 - - - +
309A ALA 3.2 0.2 - - - -
310A GLN* 1.3 75.6 - - + +
312A MSE 1.3 64.3 + - - +
314A LYS* 3.2 24.3 + - + +
315A LEU* 3.1 26.6 + - - +
321A VAL* 4.1 18.9 - - + +
324A VAL* 3.6 41.1 - - + -
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Residues in contact with MSE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.7 39.9 - - + -
92A LEU* 3.7 26.2 - - + -
129A ALA* 4.2 15.6 - - + +
130A LEU 3.8 20.9 - - - +
131A LEU* 3.9 21.8 - - + -
153A CYS 5.0 0.2 - - - -
154A LEU* 3.6 22.4 - - + +
308A ALA 3.0 24.1 + - - +
309A ALA* 3.3 6.7 + - - +
311A LEU* 1.3 76.1 - - - +
313A LEU* 1.3 58.4 + - - +
315A LEU* 3.2 10.9 + - + +
316A ILE* 2.9 34.2 + - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.5 1.8 - - - +
68A ILE* 5.1 0.9 - - + -
95A ALA* 4.3 11.0 - - + +
96A LEU* 4.2 17.3 - - + -
99A ARG* 3.7 42.8 - - + +
101A TYR* 3.9 44.9 - - + +
309A ALA 2.9 23.9 + - - +
310A GLN* 3.6 9.4 - - + +
312A MSE 1.3 77.2 - - - +
314A LYS* 1.3 57.0 + - - +
316A ILE* 3.3 8.4 + - + +
317A ASP* 2.9 37.1 + - - +
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Residues in contact with LYS 314 (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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310A GLN* 3.0 25.2 + - - +
311A LEU* 3.4 23.6 - - + +
313A LEU* 1.3 76.2 - - - +
315A LEU* 1.3 63.0 + - - +
317A ASP* 3.1 7.8 + - - +
318A GLY 3.1 4.9 + - - -
319A GLU* 3.0 54.4 + - + +
320A ASP 5.5 1.3 - - - +
321A VAL* 3.7 20.4 - - + -
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Residues in contact with LEU 315 (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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152A PRO* 4.0 19.3 - - + +
153A CYS 3.2 37.9 - - - +
154A LEU* 4.7 4.3 - - + -
166A PRO* 4.0 20.9 - - + -
311A LEU 3.1 19.4 + - - +
312A MSE 3.2 14.6 + - - +
314A LYS* 1.3 74.4 - - - +
316A ILE* 1.3 62.8 + - - +
318A GLY* 3.0 15.1 + - - -
319A GLU 4.1 9.0 - - - +
320A ASP* 5.8 0.2 - - - -
321A VAL* 3.7 28.7 - - + +
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.8 22.9 + - + +
68A ILE* 3.8 23.3 - - + -
101A TYR* 3.7 25.1 - - + +
128A ASP* 3.6 42.8 - - + +
129A ALA* 3.8 7.9 - - + -
152A PRO* 4.5 6.7 - - + -
312A MSE 2.9 22.6 + - - +
313A LEU* 3.6 10.8 - - + +
315A LEU* 1.3 77.4 - - - +
317A ASP* 1.3 61.7 + - - +
318A GLY* 3.2 1.6 + - - -
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 3.0 27.9 + - - +
99A ARG* 3.1 34.0 + - - -
313A LEU 2.9 23.1 + - - +
314A LYS* 3.1 7.1 + - - +
316A ILE* 1.3 75.0 - - - +
318A GLY* 1.3 60.0 + - - +
319A GLU* 3.4 23.5 - - - +
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Residues in contact with GLY 318 (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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315A LEU 3.0 14.6 + - - -
316A ILE 3.1 2.3 - - - -
317A ASP* 1.3 79.5 - - - +
319A GLU* 1.3 64.0 + - - +
320A ASP* 3.9 2.6 + - - +
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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
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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) + - + + + + + -
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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