Contacts of the helix formed by residues 274 - 291 (chain B) in PDB entry 4F5G
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 ASP 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASP 5.5 0.2 - - - -
104B ARG* 4.1 11.0 - - - -
272B ALA* 3.2 1.4 - - - +
273B ALA* 1.3 82.5 - - - +
275B SER* 1.3 62.8 + - - +
276B GLU* 4.1 10.0 - - - +
277B THR* 2.7 42.9 + - - -
278B VAL* 3.1 22.1 + - - +
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASP 4.4 5.9 + - - -
103B LYS* 3.4 33.9 + - - +
106B ARG* 2.9 20.4 + - - -
274B ASP* 1.3 72.5 - - - +
276B GLU* 1.3 67.3 + - - +
278B VAL* 3.3 1.3 - - - +
279B ASP* 2.9 34.0 + - - -
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ASP* 3.3 10.6 - - - +
275B SER* 1.3 79.8 - - - +
277B THR* 1.3 57.6 + - - +
279B ASP* 3.7 6.8 - - - +
280B ARG* 3.0 47.3 + - - +
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.6 34.5 - - + +
13A GLU* 4.2 9.8 - - + +
247B GLU* 5.0 1.6 - - - +
272B ALA* 3.8 16.8 - - + -
273B ALA* 4.8 4.6 - - + +
274B ASP* 2.7 32.7 + - - -
276B GLU* 1.3 75.1 - - - +
278B VAL* 1.3 59.1 + - - +
280B ARG* 3.2 23.7 + - - +
281B ALA* 2.9 28.1 + - - +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS 3.6 9.6 - - - +
104B ARG 3.3 22.7 - - - +
106B ARG* 3.5 39.3 - - + +
270B LEU* 3.4 32.1 - - + +
272B ALA* 3.6 16.7 - - + +
274B ASP 3.1 10.4 + - - +
275B SER 3.3 10.3 - - - +
277B THR* 1.3 76.4 - - - +
279B ASP* 1.3 61.6 + - - +
281B ALA* 3.4 4.1 + - + +
282B PHE* 2.8 31.8 + - - +
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Residues in contact with ASP 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 2.3 52.8 + - - -
275B SER* 2.9 21.0 + - - +
276B GLU* 3.7 6.7 - - - +
278B VAL* 1.3 73.8 - - - +
280B ARG* 1.3 65.1 + - - +
282B PHE* 3.3 5.6 + - - +
283B GLY* 3.0 19.9 + - - -
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE 4.0 1.6 + - - -
13A GLU* 3.0 30.1 + - - +
15A ILE* 2.8 24.6 + - + +
16A THR* 4.0 1.5 - - - +
17A ALA* 3.7 38.4 - - + +
18A ALA 4.9 2.8 + - - -
276B GLU* 3.0 49.9 + - - +
277B THR* 3.5 28.0 + - - +
279B ASP* 1.3 80.0 - - - +
281B ALA* 1.3 63.2 + - - +
283B GLY* 3.3 8.1 + - - -
284B GLN* 3.5 13.9 + - - +
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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
----------------------------------------------------------
12A PHE* 4.5 11.7 - - + +
15A ILE* 3.8 32.4 - - + +
123B PHE* 3.3 12.3 - - + -
270B LEU* 3.8 17.9 - - + -
277B THR 2.9 17.6 + - - +
278B VAL* 3.7 7.2 - - - +
280B ARG* 1.3 77.4 - - - +
282B PHE* 1.3 57.3 + - - +
284B GLN* 3.0 4.0 + - - +
285B MET 2.9 21.7 + - - -
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Residues in contact with PHE 282 (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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79B ASP* 3.6 19.7 - - + -
106B ARG* 3.5 37.7 - - + -
107B THR 3.3 28.0 - - - -
108B ALA* 3.6 24.5 - - + -
270B LEU* 3.9 15.2 - - + +
278B VAL 2.8 18.9 + - - +
279B ASP* 3.7 5.6 - - - +
281B ALA* 1.3 73.9 - - - +
283B GLY* 1.3 60.6 + - - +
285B MET* 3.1 12.6 + - + +
286B LYS* 2.8 65.7 + - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.9 21.7 - - - +
279B ASP 3.0 14.0 + - - -
280B ARG 3.3 4.5 + - - -
281B ALA 3.3 0.6 - - - -
282B PHE* 1.3 75.7 - - - +
284B GLN* 1.3 56.4 + - - +
286B LYS* 3.3 15.8 + - - +
287B ALA* 3.2 19.6 + - - +
290B ARG* 5.3 1.2 + - - -
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.7 10.5 - - + -
16A THR* 2.9 35.1 + - - +
17A ALA 3.7 2.2 + - - -
18A ALA* 3.4 26.7 - - - +
19A PRO* 5.2 1.5 - - - +
123B PHE* 4.2 4.9 - - + -
127B ASN* 3.3 40.4 + - - +
280B ARG 3.5 4.7 + - - +
281B ALA 3.0 9.5 + - - +
283B GLY* 1.3 75.3 - - - +
285B MET* 1.3 63.8 + - - +
287B ALA* 3.1 23.1 + - - +
288B ALA* 3.1 12.3 + - - +
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 4.7 2.2 - - - -
119B VAL* 3.7 18.2 - - + -
120B ALA* 4.2 6.5 - - - -
123B PHE* 3.7 35.3 - - + -
268B CYS* 3.4 34.1 - - - +
270B LEU* 3.3 39.5 - - + -
281B ALA 2.9 11.9 + - - +
282B PHE* 3.1 27.6 + - + +
284B GLN* 1.3 77.6 - - - +
286B LYS* 1.3 61.6 + - - +
288B ALA* 3.0 12.8 + - - +
289B ILE* 3.1 17.9 + - + +
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Residues in contact with LYS 286 (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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24A LEU* 5.2 11.7 - - - +
78B LEU* 3.2 32.1 - - + +
79B ASP* 3.9 21.9 + - + -
282B PHE* 2.8 49.8 + - + +
283B GLY* 3.4 15.6 - - - +
285B MET* 1.3 76.5 - - - +
287B ALA* 1.3 58.9 + - - +
289B ILE* 3.1 11.2 + - + +
290B ARG* 2.8 32.1 + - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 5.4 3.8 - - + -
145A ALA* 5.9 0.2 - - - +
283B GLY 3.2 11.7 + - - +
284B GLN* 3.1 23.6 + - - +
286B LYS* 1.3 76.7 - - - +
288B ALA* 1.3 61.4 + - - +
290B ARG* 3.2 21.5 + - - +
291B ALA* 3.1 23.7 + - - +
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Residues in contact with ALA 288 (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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118A ARG* 4.4 3.1 + - - -
119B VAL* 4.3 11.7 - - + +
122B ASP* 4.1 16.5 - - + +
123B PHE* 4.1 26.7 - - - +
126B LYS* 6.2 1.6 - - + -
127B ASN* 5.8 0.9 - - - +
284B GLN 3.1 10.2 + - - +
285B MET* 3.0 11.8 + - - +
287B ALA* 1.3 75.8 - - - +
289B ILE* 1.3 61.9 + - - +
291B ALA* 3.6 7.3 + - - +
292B ASN* 3.5 20.3 + - - +
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Residues in contact with ILE 289 (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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78B LEU* 3.6 26.5 - - + +
108B ALA* 3.6 30.5 - - + -
109B GLN 5.1 0.4 - - - +
110B THR* 5.1 0.4 - - + -
119B VAL* 3.8 20.9 - - + -
285B MET* 3.1 16.7 + - + +
286B LYS* 3.4 15.0 - - + +
288B ALA* 1.3 76.3 - - - +
290B ARG* 1.3 60.1 + - - +
292B ASN* 2.9 20.4 + - - -
293B TYR* 3.4 36.8 + - + +
294B SER 3.0 32.6 + - - +
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Residues in contact with ARG 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 4.2 28.8 + - - +
142A ASN* 3.9 34.1 + - - +
145A ALA* 5.0 11.0 - - + +
146A ILE* 4.1 10.6 - - - +
78B LEU* 3.5 38.2 - - + +
286B LYS* 2.8 12.3 + - - +
287B ALA* 3.5 34.5 - - - +
289B ILE* 1.3 77.8 - - - +
291B ALA* 1.3 59.3 + - - +
292B ASN 3.4 1.2 + - - +
294B SER* 4.2 15.0 + - - +
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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
----------------------------------------------------------
118A ARG* 2.8 24.5 + - - +
145A ALA* 3.5 28.5 - - + +
146A ILE* 3.5 22.7 - - - +
149A SER* 3.7 13.5 - - - -
287B ALA 3.1 13.9 + - - +
288B ALA* 4.0 6.7 - - - +
289B ILE 3.1 1.0 - - - -
290B ARG* 1.3 76.2 - - - +
292B ASN* 1.3 57.4 + - - +
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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