Contacts of the helix formed by residues 276 - 294 (chain B) in PDB entry 1A4I
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 GLY 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 5.4 3.6 - - - +
273B GLY 5.5 0.6 - - - +
274B GLY 3.3 1.0 - - - +
275B VAL* 1.3 78.6 - - - +
277B PRO* 1.3 67.8 - - - +
278B MET 3.1 1.2 + - - -
279B THR* 3.1 22.9 + - - -
302B NDP 3.7 21.6 + - - +
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Residues in contact with PRO 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY 3.7 14.6 - - - +
10B LYS* 3.8 17.0 - - + +
13B SER* 3.2 19.7 + - - +
17B ARG* 5.7 0.7 + - - -
273B GLY* 3.7 25.8 - - - +
274B GLY 3.3 19.1 - - - +
276B GLY* 1.3 90.2 - - - +
278B MET* 1.3 58.9 + - - +
279B THR* 3.3 0.6 + - - -
280B VAL* 4.5 5.1 + - - +
281B ALA* 4.6 2.8 + - - +
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Residues in contact with MET 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 3.9 5.8 - - - +
12B ILE* 3.7 22.0 - - + -
13B SER* 3.8 18.4 - - - -
16B ILE* 3.7 13.0 - - + -
151B GLY* 3.8 21.1 - - - +
154B GLU* 3.7 36.1 - - + -
155B LEU* 3.9 21.1 - - + -
274B GLY 3.6 18.4 - - - +
275B VAL 3.0 10.0 + - - +
277B PRO* 1.3 78.6 - - - +
279B THR* 1.3 64.5 + - + +
280B VAL 3.4 0.4 - - - -
281B ALA* 3.2 5.2 + - - +
282B MET* 3.0 28.1 + - + +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B CYS* 3.4 30.4 - - - +
148B THR* 3.9 23.6 - - + +
275B VAL 3.8 9.9 - - - +
276B GLY 3.1 17.8 + - - +
278B MET* 1.3 77.0 - - + +
280B VAL* 1.3 71.2 + - - +
282B MET* 3.2 3.4 + - - -
283B LEU* 3.1 19.1 + - - +
302B NDP 3.5 28.7 + - - +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 5.5 2.9 - - - -
52B TYR 5.8 0.2 - - - +
55B VAL* 4.0 24.0 - - + +
56B LYS* 4.3 25.4 - - + -
59B ALA* 3.6 31.4 - - + -
276B GLY 4.8 0.2 + - - -
277B PRO 4.5 3.8 + - - +
278B MET 3.4 0.4 - - - -
279B THR* 1.3 87.6 + - - +
281B ALA* 1.4 63.2 + - - +
283B LEU* 3.1 7.0 + - - +
284B MET* 3.0 31.8 + - + +
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Residues in contact with ALA 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 4.1 21.8 - - - +
16B ILE* 4.2 12.8 - - + -
17B ARG* 3.8 31.4 - - + +
20B LEU* 3.9 4.1 - - - +
277B PRO 4.6 1.6 + - - -
278B MET 3.2 10.3 + - - +
280B VAL* 1.4 79.0 - - - +
282B MET* 1.3 62.0 + - + +
284B MET* 3.2 7.0 + - - +
285B GLN* 2.8 28.4 + - - +
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.8 33.4 - - + -
147B CYS* 3.5 31.9 - - + +
150B LYS* 3.7 28.7 - - + +
151B GLY* 3.5 19.1 - - - +
154B GLU* 4.6 5.6 - - + -
278B MET* 3.0 22.4 + - + +
279B THR 3.4 8.1 - - - +
280B VAL 3.2 0.2 - - - -
281B ALA* 1.3 80.2 - - + +
283B LEU* 1.3 60.1 + - - +
285B GLN* 3.2 20.9 + - - +
286B SER* 2.9 32.2 + - - -
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.5 5.2 - - + -
56B LYS* 3.8 35.0 - - + +
98B LEU* 3.7 19.7 - - + -
124B VAL* 3.6 35.9 - - + +
125B ASP* 4.0 11.9 - - - +
147B CYS* 4.3 9.3 - - + +
279B THR 3.1 12.3 + - - +
280B VAL* 3.1 8.9 + - + +
282B MET* 1.3 74.8 - - - +
284B MET* 1.3 79.4 + - + +
286B SER* 3.3 5.3 + - - -
287B THR* 2.9 34.3 + - - +
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Residues in contact with MET 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 5.7 0.2 - - - -
20B LEU* 3.7 5.8 - - + -
38B LEU* 4.1 11.7 - - + -
56B LYS 3.3 28.0 - - - +
59B ALA* 4.4 6.7 - - + -
60B ALA* 3.7 27.4 - - + +
63B ILE* 3.6 30.7 - - + -
65B ILE* 4.0 11.2 - - + -
280B VAL* 3.0 22.6 + - + +
281B ALA* 3.2 7.4 + - - +
283B LEU* 1.3 105.8 - - + +
285B GLN* 1.3 62.9 + - - +
287B THR* 3.2 5.4 + - - -
288B VAL* 3.0 26.9 + - - +
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.2 16.5 - - + +
20B LEU* 3.5 24.3 - - + +
23B GLN* 5.6 2.6 - - - +
150B LYS* 3.3 18.0 + - - +
154B GLU* 5.1 10.1 + - - +
281B ALA 2.8 13.8 + - - +
282B MET* 3.2 26.4 + - + +
284B MET* 1.3 76.6 - - - +
286B SER* 1.3 56.0 + - - +
288B VAL* 3.3 3.3 + - - +
289B GLU* 3.0 47.1 + - + +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 3.8 27.4 + - - -
144B PHE* 3.4 22.9 - - - -
145B ILE 4.1 6.8 + - - -
147B CYS* 6.1 0.2 - - - -
150B LYS* 3.6 18.0 + - - +
282B MET 2.9 13.3 + - - -
283B LEU* 3.6 8.9 - - - -
285B GLN* 1.3 75.3 - - - +
287B THR* 1.3 59.2 + - - +
289B GLU* 3.4 12.7 + - - +
290B SER 2.9 22.5 + - - -
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Residues in contact with THR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO* 5.5 2.2 - - + -
37B ARG 4.5 11.9 - - - +
38B LEU* 3.7 44.2 - - + +
65B ILE* 4.1 21.3 - - + -
95B HIS* 4.8 1.6 - - + +
96B GLY 5.3 2.7 - - - +
124B VAL* 4.0 13.1 - - + +
283B LEU* 2.9 17.1 + - - +
284B MET* 3.2 12.2 + - - -
286B SER* 1.3 73.4 - - - +
288B VAL* 1.3 61.7 - - - +
290B SER* 3.2 3.7 + - - -
291B ALA* 2.9 27.6 + - - +
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 4.1 17.7 - - + -
23B GLN* 3.9 13.0 - - + +
24B VAL* 3.7 27.1 - - + -
27B LEU* 4.6 8.7 - - + -
36B PRO* 5.6 2.0 - - + -
65B ILE* 4.0 14.4 - - + -
284B MET 3.0 19.8 + - - +
285B GLN 3.3 4.0 + - - +
287B THR* 1.3 75.3 - - - +
289B GLU* 1.3 58.6 + - - +
291B ALA* 3.1 7.1 + - - +
292B LYS* 2.8 57.5 + - + +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B CYS 4.6 7.8 - - - +
144B PHE* 4.4 9.5 - - - -
145B ILE* 5.9 0.2 - - - +
150B LYS* 2.9 33.3 + - - -
285B GLN* 3.0 29.5 + - + +
286B SER* 3.5 16.2 + - - +
288B VAL* 1.3 76.2 - - - +
290B SER* 1.3 64.8 - - - +
292B LYS* 3.3 9.2 + - - +
293B ARG* 3.1 44.3 + - - +
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Residues in contact with SER 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 2.8 31.9 + - - +
121B GLU 3.2 15.9 + - - -
124B VAL* 4.4 4.5 - - - -
144B PHE* 3.6 17.7 - - - -
286B SER 2.9 10.9 + - - -
287B THR 3.2 7.4 + - - -
289B GLU* 1.3 74.4 - - - +
291B ALA* 1.3 68.1 - - - +
293B ARG* 3.2 13.8 + - - +
294B PHE* 3.0 22.5 + - - +
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 5.4 1.8 - - + -
34B PHE* 3.5 24.8 - - + -
36B PRO* 3.9 23.1 - - + -
37B ARG 5.1 0.2 - - - +
95B HIS* 3.9 19.9 - - + +
287B THR 2.9 17.0 + - - +
288B VAL* 3.7 5.6 - - - +
290B SER* 1.3 78.6 - - - +
292B LYS* 1.3 57.2 + - + +
294B PHE* 3.2 4.0 + - - +
295B LEU* 3.0 28.4 + - - +
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 3.0 32.1 + - - +
27B LEU* 3.7 34.3 - - + +
288B VAL* 2.8 42.0 + - + +
289B GLU* 3.7 7.6 - - - +
290B SER 3.2 0.2 - - - -
291B ALA* 1.3 72.9 - - - +
293B ARG* 1.3 62.5 + - + +
295B LEU* 3.2 9.5 + - + +
296B GLU* 3.1 23.9 + - - +
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLU* 5.5 3.2 + - - +
141B ASN 4.6 3.0 + - - -
142B ASP* 3.4 49.8 + - - +
143B CYS 4.5 2.4 + - - -
144B PHE* 3.1 44.7 - - - -
289B GLU* 3.1 27.8 + - - +
290B SER* 3.2 14.7 + - - +
292B LYS* 1.3 76.8 - - + +
294B PHE* 1.3 63.6 + - - +
296B GLU* 3.5 20.0 + - - +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.8 14.8 - + - -
92B SER* 3.4 35.0 - - - -
94B VAL 5.9 1.1 - - - -
95B HIS* 3.5 35.2 - + + -
122B LYS* 6.5 1.3 - - - -
290B SER* 3.0 12.7 + - - +
291B ALA 3.5 7.0 - - - +
293B ARG* 1.3 78.9 - - - +
295B LEU* 1.3 66.2 + - - +
296B GLU 3.3 8.8 + - - +
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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