Contacts of the helix formed by residues 274 - 291 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ASP 5.1 0.7 - - - -
103A LYS 4.4 3.4 - - - -
104A ARG* 3.9 10.5 - - - -
272A ALA* 3.2 1.6 - - - +
273A ALA* 1.3 84.1 - - - +
275A SER* 1.3 65.9 + - - +
276A GLU* 3.4 15.5 - - - +
277A THR* 2.6 35.6 + - - -
278A VAL* 3.0 22.6 + - - +
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP 4.3 5.2 + - - -
103A LYS* 3.3 35.3 + - - +
106A ARG* 2.9 20.3 + - - -
274A ASP* 1.3 74.7 - - - +
276A GLU* 1.3 64.4 + - - +
278A VAL* 3.2 5.1 - - - +
279A ASP* 2.9 26.3 + - - +
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 3.4 14.7 - - - +
275A SER* 1.3 78.5 - - - +
277A THR* 1.3 76.3 + - - +
279A ASP* 3.4 9.3 + - - +
280A ARG* 2.9 50.3 + - - +
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Residues in contact with THR 277 (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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247A GLU* 5.2 1.3 - - - +
272A ALA* 3.7 18.2 - - + -
273A ALA* 4.7 6.4 - - + +
274A ASP* 2.6 30.8 + - - -
276A GLU* 1.3 89.9 + - - +
278A VAL* 1.3 65.4 + - - +
280A ARG* 3.2 17.9 + - - +
281A ALA* 3.0 21.3 + - - +
12B PHE* 3.6 29.1 - - + +
13B GLU* 4.2 7.1 - - + +
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Residues in contact with VAL 278 (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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103A LYS 3.9 0.4 - - - +
104A ARG 3.4 25.1 - - - +
106A ARG* 3.4 39.3 - - + +
270A LEU* 3.5 31.0 - - + +
272A ALA* 3.7 17.5 - - + +
274A ASP 3.0 13.1 + - - +
275A SER* 3.2 16.4 - - - +
277A THR* 1.3 77.1 - - - +
279A ASP* 1.3 52.5 + - - +
281A ALA* 3.6 3.0 - - + +
282A PHE* 2.7 38.3 + - - +
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Residues in contact with ASP 279 (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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106A ARG* 2.9 42.2 + - - +
275A SER* 2.9 16.4 + - - +
276A GLU* 3.5 9.9 - - - +
277A THR 3.1 0.2 - - - -
278A VAL* 1.3 75.5 - - - +
280A ARG* 1.3 59.6 + - - +
282A PHE* 3.8 6.6 - - - +
283A GLY* 2.9 26.7 + - - -
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLU* 2.9 37.5 + - - +
277A THR* 3.2 34.6 + - - +
279A ASP* 1.3 75.7 - - + +
281A ALA* 1.3 63.8 + - - +
283A GLY* 3.4 1.6 + - - -
284A GLN* 3.4 22.7 + - - +
12B PHE 3.9 2.4 + - - -
13B GLU* 2.8 31.3 + - - +
14B ASN* 3.9 1.4 - - - +
15B ILE* 2.8 49.8 + - + +
16B THR* 4.5 1.3 - - - +
17B ALA* 4.0 29.7 - - + +
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Residues in contact with ALA 281 (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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123A PHE* 3.3 20.7 - - + -
270A LEU* 3.8 17.9 - - + -
277A THR 3.0 13.2 + - - +
278A VAL* 3.6 10.5 - - + +
280A ARG* 1.3 76.8 - - - +
282A PHE* 1.3 59.5 + - - +
284A GLN* 3.1 2.9 + - - -
285A MET* 2.9 23.7 + - - +
12B PHE* 4.3 14.4 - - + -
15B ILE* 3.9 21.5 - - + +
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Residues in contact with PHE 282 (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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79A ASP* 3.5 22.7 - - + -
106A ARG* 3.5 38.1 - - + -
107A THR 3.3 26.7 - - - -
108A ALA* 3.5 26.5 - - + -
270A LEU* 4.0 15.7 - - + +
278A VAL 2.7 22.6 + - - +
279A ASP* 3.8 7.4 - - - +
281A ALA* 1.3 71.2 - - - +
283A GLY* 1.3 59.9 + - - +
285A MET* 3.1 12.5 + - + +
286A LYS* 2.8 61.5 + - + +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASP 2.9 16.2 + - - -
280A ARG* 3.9 2.7 - - - -
281A ALA 3.3 0.4 - - - -
282A PHE* 1.3 76.1 - - - +
284A GLN* 1.3 56.1 + - - +
286A LYS* 3.3 16.7 + - - +
287A ALA* 3.1 20.3 + - - +
290A ARG* 5.4 1.0 + - - -
18B ALA* 3.8 21.7 - - - +
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Residues in contact with GLN 284 (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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123A PHE* 4.1 5.6 - - + -
127A ASN* 3.3 38.8 + - - +
280A ARG 3.4 4.3 + - - +
281A ALA 3.1 8.5 + - - +
283A GLY* 1.3 73.9 - - - +
285A MET* 1.3 66.2 + - - +
287A ALA* 3.1 19.7 + - - +
288A ALA* 3.0 20.3 + - - +
15B ILE* 3.7 11.4 - - + -
16B THR* 2.9 33.9 + - - +
17B ALA 3.9 1.4 + - - -
18B ALA* 3.6 21.3 - - - +
19B PRO* 5.1 2.2 - - - +
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Residues in contact with MET 285 (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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108A ALA* 4.5 2.2 - - - -
119A VAL* 3.6 19.7 - - + -
120A ALA* 4.3 3.4 - - - -
123A PHE* 3.6 35.4 - - + -
268A CYS* 3.5 37.0 - - - +
270A LEU* 3.4 37.9 - - + -
281A ALA 2.9 13.1 + - - +
282A PHE* 3.1 22.6 + - + +
284A GLN* 1.3 77.2 - - - +
286A LYS* 1.3 62.8 + - - +
288A ALA* 3.0 4.4 + - - +
289A ILE* 2.9 29.0 + - + +
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Residues in contact with LYS 286 (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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78A LEU* 3.3 27.5 - - + +
79A ASP* 3.8 22.3 + - - +
282A PHE* 2.8 52.7 + - + +
283A GLY* 3.3 15.4 - - - +
284A GLN 3.2 0.2 - - - -
285A MET* 1.3 77.4 - - - +
287A ALA* 1.3 56.0 + - - +
289A ILE* 3.1 12.3 + - + +
290A ARG* 2.8 36.2 + - - +
24B LEU* 5.7 6.7 - - - +
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Residues in contact with ALA 287 (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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283A GLY 3.1 10.8 + - - +
284A GLN* 3.1 25.7 + - - +
286A LYS* 1.3 77.4 - - - +
288A ALA* 1.3 62.6 + - - +
290A ARG* 3.2 25.1 + - - +
291A ALA* 3.1 23.9 + - - +
18B ALA* 5.1 4.5 - - + -
145B ALA* 5.8 0.7 - - - +
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Residues in contact with ALA 288 (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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119A VAL* 4.5 8.6 - - + +
122A ASP* 4.2 15.7 - - + +
123A PHE* 4.0 29.4 - - + +
126A LYS* 6.2 2.0 - - + -
127A ASN* 5.5 0.9 - - - +
284A GLN 3.0 11.3 + - - +
285A MET* 3.0 10.6 + - - +
287A ALA* 1.3 75.6 - - - +
289A ILE* 1.3 63.3 + - - +
291A ALA* 3.5 7.5 + - - +
292A ASN* 3.4 21.1 + - - +
118B ARG* 4.5 2.1 + - - -
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Residues in contact with ILE 289 (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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78A LEU* 3.8 23.6 - - + +
108A ALA* 3.8 29.6 - - + -
109A GLN 5.1 0.7 - - - +
110A THR* 5.3 0.2 - - + -
119A VAL* 3.8 20.4 - - + -
285A MET* 2.9 23.8 + - + +
286A LYS* 3.1 16.4 + - + +
288A ALA* 1.3 75.6 - - - +
290A ARG* 1.3 59.4 + - - +
292A ASN* 2.9 20.5 + - - -
293A TYR* 3.3 21.0 + - + +
294A SER 2.8 51.3 + - - +
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Residues in contact with ARG 290 (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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78A LEU* 3.5 29.0 - - + +
283A GLY 5.4 1.0 + - - -
286A LYS* 2.8 19.8 + - - +
287A ALA* 3.2 34.7 + - - +
289A ILE* 1.3 76.8 - - - +
291A ALA* 1.3 58.6 + - - +
292A ASN 3.1 2.0 + - - +
294A SER* 3.5 17.9 + - - +
21B ASP* 5.2 12.2 + - - +
142B ASN* 3.8 32.1 + - - +
145B ALA* 5.1 10.7 - - + +
146B ILE* 4.1 10.6 - - - +
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Residues in contact with ALA 291 (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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287A ALA 3.1 14.9 + - - +
288A ALA* 4.0 7.4 - - - +
289A ILE 3.1 0.4 - - - -
290A ARG* 1.3 76.6 - - - +
292A ASN* 1.3 58.1 + - - +
118B ARG* 2.9 25.6 + - - +
145B ALA* 3.5 28.5 - - + +
146B ILE* 3.5 21.7 - - - +
149B SER* 3.5 13.1 + - - -
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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