Contacts of the helix formed by residues 306 - 323 (chain A) in PDB entry 1L7R
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 PRO 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 6.0 3.4 - - + -
285A TRP* 3.7 17.9 - - + -
302A ALA 5.3 3.4 - - - +
304A THR 2.8 10.1 - - - +
305A TYR* 1.3 85.0 - - + +
307A ILE* 1.3 59.1 + - - +
308A GLN 3.3 2.7 - - - -
309A GLU* 3.2 33.2 + - + +
310A ALA* 2.8 30.0 + - + +
345A TRP* 4.3 16.6 - - + +
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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
----------------------------------------------------------
53A SER 3.4 25.4 - - - +
54A THR* 3.9 19.5 - - + +
56A SER 4.1 2.9 - - - +
57A THR* 3.8 19.5 - - - +
58A ASN* 3.5 30.1 - - - +
305A TYR* 2.9 28.5 + - + +
306A PRO* 1.3 72.5 - - - +
308A GLN* 1.3 58.0 + - + +
310A ALA* 3.4 2.0 + - - +
311A THR* 2.7 36.2 + - - -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.3 23.1 + - - +
61A GLU* 3.2 28.1 + - - +
306A PRO 3.3 0.8 - - - -
307A ILE* 1.3 83.9 - - + +
309A GLU* 1.3 59.9 + - + +
311A THR* 3.1 5.2 + - - -
312A THR* 3.0 35.1 + - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO* 3.2 28.5 + - + +
308A GLN* 1.3 79.0 - - + +
310A ALA* 1.3 58.0 + - - +
312A THR* 3.3 7.8 + - - +
313A MET* 2.9 29.1 + - - +
336A ARG* 4.2 18.7 + - - -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER 3.9 6.7 - - - +
57A THR* 4.2 2.2 - - + -
305A TYR* 3.6 26.9 - - + +
306A PRO* 2.8 20.8 + - + +
307A ILE 3.6 4.3 - - - +
309A GLU* 1.3 75.0 - - - +
311A THR* 1.3 61.1 + - - +
313A MET* 3.3 6.6 + - - +
314A HIS* 2.8 42.2 + - + +
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Residues in contact with THR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 3.6 8.9 - - - +
58A ASN* 2.8 45.8 + - + +
61A GLU* 3.6 28.3 - - - +
62A PHE* 3.6 15.9 - - + -
307A ILE 2.7 19.9 + - - -
308A GLN* 3.1 14.1 + - - -
310A ALA* 1.3 77.4 - - - +
312A THR* 1.3 56.5 + - - +
314A HIS* 3.3 0.8 + - - -
315A LYS* 2.9 28.5 + - - +
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 4.8 5.6 + - - -
308A GLN* 3.0 28.8 + - - +
309A GLU* 3.7 10.4 - - - -
311A THR* 1.3 76.6 - - - +
313A MET* 1.3 62.3 + - - +
315A LYS* 3.4 10.1 + - - +
316A ALA* 3.1 24.3 + - + +
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU* 3.9 22.0 - - + -
279A ARG* 3.7 32.5 - - + -
280A LEU 5.2 1.3 - - - +
281A VAL* 3.8 27.4 - - + -
309A GLU 2.9 17.1 + - - +
310A ALA* 3.7 7.4 - - - +
312A THR* 1.3 75.9 - - - +
314A HIS* 1.3 65.5 + - - +
316A ALA* 3.3 6.5 + - - +
317A PHE* 2.9 22.7 + - + +
329A LEU* 4.5 2.9 - - + +
332A VAL* 4.0 33.2 - - + -
333A PRO* 4.7 4.5 - - + +
336A ARG* 6.1 1.6 - - + -
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 5.4 2.0 + - - -
57A THR* 3.8 20.9 - - + +
62A PHE* 3.6 19.1 - + + -
114A PHE* 4.2 14.6 - - + +
115A GLY 5.7 0.4 + - - -
138A ALA* 3.6 34.6 + - + +
140A SER* 6.1 2.9 - - - -
252A LEU* 3.6 30.1 + - + +
254A THR* 4.7 8.7 + - - -
305A TYR* 5.0 4.0 - - - -
310A ALA* 2.8 36.7 + - + +
313A MET* 1.3 77.5 - - - +
315A LYS* 1.3 59.1 + - - +
317A PHE* 3.2 1.9 + - - +
318A PHE* 2.9 42.1 + + + -
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 3.8 22.9 - - + +
62A PHE* 3.9 21.9 - - + -
65A ASP* 3.4 39.6 + - + +
67A TYR* 4.5 5.4 - - + -
311A THR 2.9 17.6 + - - +
312A THR* 3.8 9.6 - - - +
314A HIS* 1.3 78.0 - - - +
316A ALA* 1.3 52.7 + - - +
318A PHE* 3.3 5.0 + - - +
319A ASP* 2.7 62.8 + - - +
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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 THR* 3.1 19.0 + - + +
313A MET* 3.6 6.7 - - - +
315A LYS* 1.3 76.6 - - - +
317A PHE* 1.3 58.1 + - - +
319A ASP* 3.2 8.0 + - - -
320A ARG* 2.9 26.9 + - - +
328A ALA* 3.4 31.6 - - - +
329A LEU* 3.8 11.0 - - + -
332A VAL* 4.9 5.4 - - + -
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Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.7 15.5 - - + -
137A ILE 3.4 21.1 - - - -
250A PRO* 3.6 9.9 - - + -
251A ALA 3.5 24.7 - - - -
252A LEU* 3.5 26.7 - - + -
277A ASP* 3.6 22.4 - - - -
279A ARG* 4.1 18.8 - - + -
313A MET* 2.9 14.6 + - + +
314A HIS 3.2 8.0 + - - +
316A ALA* 1.3 78.1 - - - +
318A PHE* 1.3 76.9 + + - +
320A ARG* 3.4 0.5 + - - +
321A HIS* 3.1 46.2 + + - +
329A LEU* 3.6 15.4 - - + +
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.8 38.4 - - + -
62A PHE* 4.5 6.1 - + - -
67A TYR* 3.0 27.4 + + + +
113A MET 3.5 25.6 - - - -
114A PHE* 4.1 11.9 - - + -
136A ALA* 4.4 11.9 - - + -
138A ALA* 4.1 9.4 - - + -
314A HIS* 2.9 40.7 + + + +
315A LYS* 3.9 3.8 - - - +
317A PHE* 1.3 94.3 - + - +
319A ASP* 1.3 58.8 + - - +
322A LEU* 2.7 50.9 + - + +
323A ARG 3.4 0.2 + - - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 4.3 2.4 - - - +
67A TYR* 2.7 30.4 + - - -
315A LYS* 2.7 51.8 + - - +
316A ALA* 3.2 7.6 + - - +
318A PHE* 1.3 72.3 - - - +
320A ARG* 1.3 61.4 + - - +
323A ARG* 3.0 38.3 + - - +
325A GLU* 3.1 38.6 + - - +
328A ALA* 3.9 6.0 - - + +
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA 2.9 16.1 + - - +
317A PHE 3.6 4.7 - - - +
319A ASP* 1.3 77.1 - - - +
321A HIS* 1.3 85.2 + - + +
324A GLY* 3.3 22.3 + - - -
325A GLU 3.1 26.7 - - - +
326A THR* 3.5 37.3 + - - +
328A ALA* 3.7 6.3 - - + +
329A LEU* 4.0 18.2 - - + +
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Residues in contact with HIS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN* 4.5 1.4 - - - +
135A LYS* 3.4 33.3 - - - +
136A ALA* 4.0 8.1 - - + -
250A PRO* 3.5 28.5 - - + +
277A ASP* 2.6 37.3 + - + -
317A PHE* 3.1 44.6 + + - +
320A ARG* 1.3 105.4 + - + +
322A LEU* 1.3 61.1 + - + +
324A GLY* 4.4 1.4 + - - -
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 4.2 11.5 - - + +
37A VAL 3.8 9.2 - - - +
38A LEU* 3.8 14.4 - - + -
67A TYR* 4.1 11.9 - - + -
108A ASP* 4.8 1.4 - - - +
110A ASN* 3.2 47.9 + - + +
111A VAL 3.7 5.6 - - - +
112A GLY* 3.6 24.5 - - - +
135A LYS* 4.0 16.6 - - + -
136A ALA* 4.0 11.9 - - + +
318A PHE* 2.7 42.4 + - + +
321A HIS* 1.3 77.8 - - - +
323A ARG* 1.3 59.8 + - - +
324A GLY 3.6 0.7 - - - -
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Residues in contact with ARG 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PRO* 3.9 22.4 - - + +
65A ASP* 3.1 29.3 + - - -
66A GLY* 3.6 22.0 + - - -
67A TYR* 3.6 22.4 + - + +
318A PHE 3.4 0.2 + - - -
319A ASP* 3.0 33.3 + - - +
322A LEU* 1.3 79.2 - - - +
324A GLY* 1.3 63.3 + - - +
325A GLU* 3.1 28.2 + - + +
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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) + - + + + + + -
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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