Contacts of the helix formed by residues 1419 - 1424 (chain A) in PDB entry 4C8D
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 GLY1419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1394A HIS 5.0 2.7 - - - -
1396A PRO* 3.9 13.2 - - - +
1418A SER* 1.3 76.8 - - - +
1420A VAL* 1.3 63.8 + - - +
1421A HIS* 3.3 20.0 + - - -
1422A LYS* 3.2 28.4 + - - +
1423A LYS* 4.1 3.3 + - - +
1677A LEU 5.2 0.6 + - - -
1678A GLY 3.3 6.7 + - - -
1679A ASP* 4.4 0.2 + - - -
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Residues in contact with VAL1420 (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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1396A PRO* 4.1 23.1 - - + -
1417A VAL* 4.0 13.5 - - + +
1419A GLY* 1.3 75.4 - - - +
1421A HIS* 1.3 63.7 + - - +
1423A LYS* 3.1 19.2 + - + +
1424A LEU* 3.6 16.1 + - + +
1505A LEU* 6.3 1.3 - - + -
1508A ASN* 4.0 21.1 - - + +
1509A LEU* 5.4 0.7 - - + -
1510A PRO* 4.3 11.7 - - + -
1569A VAL* 3.8 23.3 - - + -
1678A GLY 2.9 17.8 + - - +
1680A ALA* 4.1 15.5 - - + -
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Residues in contact with HIS1421 (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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1419A GLY* 3.8 13.9 - - - -
1420A VAL* 1.3 78.8 - - - +
1422A LYS* 1.3 94.8 + - + +
1423A LYS 3.1 1.0 + - - -
1424A LEU* 3.3 30.5 + - + +
1426A SER* 5.0 5.2 + - - -
1569A VAL* 5.6 0.2 - - - +
1570A MET 4.9 1.8 - - - +
1571A VAL 5.1 3.1 - - - +
1608A GLU* 6.0 0.9 - - - -
1677A LEU* 3.8 44.1 + - + +
1678A GLY* 3.3 27.1 - - - +
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Residues in contact with LYS1422 (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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1419A GLY* 3.2 16.7 + - - +
1420A VAL 3.2 1.2 - - - -
1421A HIS* 1.3 107.7 - - + +
1423A LYS* 1.3 64.1 + - + +
1424A LEU 4.7 2.1 - - - +
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Residues in contact with LYS1423 (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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1395A ASP* 4.6 4.4 + - - -
1396A PRO* 4.0 33.0 - - + -
1397A SER* 3.6 27.9 + - - -
1419A GLY 4.2 3.4 - - - +
1420A VAL* 3.1 11.4 + - - +
1421A HIS 3.0 0.6 - - - -
1422A LYS* 1.3 83.4 - - + +
1424A LEU* 1.3 64.1 + - - +
1425A LYS* 5.5 0.7 - - - +
1504A ASP* 4.6 0.7 - - - +
1508A ASN* 3.6 41.7 + - + +
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Residues in contact with LEU1424 (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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1420A VAL* 3.6 24.7 - - + +
1421A HIS* 3.3 21.8 + - - +
1422A LYS 4.7 2.3 - - - +
1423A LYS* 1.3 82.3 - - - +
1425A LYS* 1.3 61.7 + - - +
1426A SER* 3.4 8.4 + - - +
1429A TRP* 3.9 18.6 - - + +
1504A ASP* 3.4 39.0 - - - +
1505A LEU* 4.2 11.0 - - + -
1508A ASN* 4.1 10.5 - - + +
1569A VAL* 5.1 1.1 - - + -
1571A VAL* 3.6 35.9 - - + +
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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