Contacts of the helix formed by residues 1400 - 1406 (chain A) in PDB entry 5IRC
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 PHE1400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283A TYR* 3.7 39.0 - + + -
1321A MET* 3.9 24.5 - - + -
1322A LYS* 3.8 21.3 - - + -
1325A PHE* 4.6 4.7 - + - -
1375A VAL* 4.1 13.0 - - + -
1379A LEU* 4.1 24.2 - - + -
1396A LEU* 2.9 14.6 + - + +
1397A SER* 3.1 0.9 + - - -
1398A ILE 3.4 1.4 + - - -
1399A CYS* 1.3 83.7 - - - +
1401A TRP* 1.3 67.2 + - - +
1402A PRO* 3.3 3.8 - - - -
1403A THR* 3.0 24.6 + - + -
1404A LEU* 3.3 36.8 + - + +
1425A ILE* 5.8 1.1 - - + -
65F ASP* 3.5 6.2 + - - -
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Residues in contact with TRP1401 (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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1397A SER* 2.9 28.7 + - - +
1400A PHE* 1.3 77.9 - - - +
1402A PRO* 1.4 74.6 - - + +
1404A LEU* 3.1 7.8 + - - +
1405A MET* 3.0 31.9 + - + +
1407A PRO* 3.5 39.3 - - + -
1409A PHE* 4.2 5.8 - + - -
1418A THR* 3.5 39.9 - - + -
1421A TYR* 3.5 25.4 - + + -
1422A GLN* 3.5 37.9 + - + +
1425A ILE* 3.5 34.3 - - + +
66F TYR* 3.6 16.9 + + - -
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Residues in contact with PRO1402 (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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1398A ILE 4.1 7.2 - - - +
1400A PHE 3.5 4.0 - - - -
1401A TRP* 1.4 123.9 - - + +
1403A THR* 1.3 57.2 + - - +
1406A ARG* 2.7 30.1 + - - -
1407A PRO* 3.5 17.4 - - + +
1409A PHE* 4.3 0.9 - - + -
65F ASP* 3.4 32.1 - - + +
66F TYR* 3.8 24.9 - - + -
68F ARG* 5.0 1.1 + - - +
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Residues in contact with THR1403 (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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1322A LYS* 3.6 30.0 - - - +
1325A PHE* 3.5 40.1 - - + +
1326A SER* 4.3 10.9 + - - +
1331A PRO* 5.4 0.7 - - - +
1332A LEU 5.2 2.1 + - - -
1400A PHE* 3.0 29.3 + - + -
1402A PRO* 1.3 79.2 - - - +
1404A LEU* 1.3 61.2 + - - +
1406A ARG* 4.5 5.5 + - - +
64F GLU* 5.5 1.0 - - - +
65F ASP* 2.6 28.5 + - - +
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Residues in contact with LEU1404 (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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1325A PHE* 4.5 10.5 - - + -
1331A PRO* 3.6 1.3 - - - +
1332A LEU* 3.4 36.0 + - + -
1333A VAL* 3.1 38.3 + - + +
1372A PHE* 4.1 21.1 - - + -
1375A VAL* 4.6 11.0 - - + -
1376A ILE* 4.4 14.1 - - + -
1379A LEU* 5.2 1.1 - - + -
1400A PHE* 3.3 39.2 + - + +
1401A TRP* 3.1 10.8 + - - +
1403A THR* 1.3 80.2 - - - +
1405A MET* 1.3 60.1 + - + +
1425A ILE* 4.8 10.1 - - + -
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Residues in contact with MET1405 (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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1331A PRO* 3.7 2.3 - - - +
1333A VAL* 4.1 14.8 - - + -
1335A TYR* 3.4 6.2 - - - -
1338A GLN* 2.9 41.9 + - + +
1341A LEU* 4.1 26.2 - - + -
1401A TRP* 3.0 26.3 + - + +
1404A LEU* 1.3 84.2 - - + +
1406A ARG* 1.3 75.4 + - - +
1407A PRO* 3.6 0.8 - - + -
1421A TYR* 3.8 39.5 - - + +
1424A ILE* 4.6 6.3 - - + -
1425A ILE* 3.6 31.4 - - + -
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Residues in contact with ARG1406 (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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1325A PHE 3.0 26.1 + - - -
1326A SER* 3.3 16.5 + - - +
1328A LEU 2.8 31.4 + - - -
1329A PRO 3.2 18.6 + - - -
1330A ASP* 3.6 12.7 + - - +
1331A PRO* 3.7 18.3 - - + +
1335A TYR* 2.7 31.7 + - - +
1402A PRO 2.7 19.6 + - - +
1403A THR 4.5 4.1 + - - +
1404A LEU 3.8 0.2 - - - -
1405A MET* 1.3 73.9 - - - +
1407A PRO* 1.3 70.4 - - - +
68F ARG* 3.4 17.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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