Contacts of the helix formed by residues 1418 - 1426 (chain A) in PDB entry 2YVI
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 SER1418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1415A LEU* 2.9 20.0 + - - -
1417A LEU* 1.3 77.5 - - - +
1419A TRP* 1.3 63.7 + - - +
1420A ALA 3.3 0.9 - - - -
1421A GLU* 3.2 15.1 + - - +
1422A LEU* 3.0 21.0 + - - +
1475A ILE* 3.9 6.4 + - - +
1477A ARG* 2.8 42.6 + - - +
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Residues in contact with TRP1419 (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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1415A LEU* 3.9 21.5 + - + +
1416A GLY 3.3 21.5 + - - -
1417A LEU 3.3 4.6 - - - -
1418A SER* 1.3 77.2 - - - +
1420A ALA* 1.3 68.1 + - + +
1422A LEU* 3.3 3.8 + - - +
1423A ALA* 2.9 28.2 + - + +
1433A ILE* 3.5 42.8 - - + -
1436A ILE* 3.6 28.3 - - + -
1437A ARG* 3.8 19.5 - - + -
1444A LEU* 3.9 10.7 - - + +
1447A GLN* 2.8 44.4 + - + +
1448A SER* 3.5 28.3 - - - +
1451A LEU* 4.2 19.3 - - + +
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Residues in contact with ALA1420 (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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1417A LEU 4.0 6.0 + - - +
1418A SER 3.3 0.8 - - - -
1419A TRP* 1.3 100.5 - - + +
1421A GLU* 1.3 65.8 + - - +
1423A ALA* 3.3 4.6 + - - +
1424A ARG* 3.1 29.7 + - + +
1433A ILE* 3.9 6.3 - - + +
1437A ARG* 3.8 25.8 - - - +
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Residues in contact with GLU1421 (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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1417A LEU 4.9 1.0 + - - +
1418A SER* 3.2 15.4 + - - +
1420A ALA* 1.3 76.6 - - - +
1422A LEU* 1.3 65.5 - - - +
1424A ARG* 3.2 15.6 + - + +
1425A GLU* 2.9 22.3 + - + +
1474A SER 4.9 0.7 - - - +
1475A ILE* 3.5 41.8 - - + +
1476A ASP* 5.3 1.4 - - - +
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Residues in contact with LEU1422 (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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1411A ILE* 5.1 1.8 - - + -
1415A LEU* 3.8 29.2 - - + -
1418A SER 3.0 13.0 + - - +
1419A TRP* 3.5 8.1 - - - +
1421A GLU* 1.3 78.1 - - - +
1423A ALA* 1.3 57.2 + - - +
1425A GLU* 3.0 5.6 + - - +
1426A LEU* 2.8 51.0 + - + +
1451A LEU* 4.3 10.5 - - + -
1452A LEU* 4.6 2.5 - - + -
1468A LEU* 4.5 11.2 - - + +
1471A ALA* 3.4 42.0 - - + +
1472A LEU* 3.9 17.7 - - + +
1475A ILE* 3.9 11.8 - - + +
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Residues in contact with ALA1423 (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 TRP* 2.9 17.6 + - + +
1420A ALA* 3.4 11.2 - - - +
1422A LEU* 1.3 77.0 - - - +
1424A ARG* 1.3 63.2 + - - +
1426A LEU* 3.2 7.4 + - - -
1427A GLN 3.2 0.3 + - - -
1428A PHE* 3.0 35.0 + - + -
1433A ILE* 3.6 24.0 - - + -
1451A LEU* 3.7 24.9 - - + +
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Residues in contact with ARG1424 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1420A ALA* 3.1 19.3 + - - +
1421A GLU* 3.5 16.3 - - + +
1422A LEU 3.2 0.2 - - - -
1423A ALA* 1.3 74.8 - - - +
1425A GLU* 1.3 59.1 + - - +
1427A GLN* 2.8 22.7 + - - +
1428A PHE 4.5 6.3 - - - +
1430A VAL* 6.1 4.5 - - + +
1433A ILE* 3.6 17.7 - - + -
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Residues in contact with GLU1425 (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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1421A GLU* 2.9 13.3 + - - +
1422A LEU* 3.3 11.2 - - - +
1424A ARG* 1.3 77.1 - - - +
1426A LEU* 1.3 58.8 + - - +
1427A GLN* 3.1 9.4 + - - +
1471A ALA* 3.7 35.2 - - + +
1474A SER* 4.0 20.5 + - - +
1475A ILE* 4.3 10.2 - - + +
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Residues in contact with LEU1426 (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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1422A LEU* 2.8 39.6 + - + +
1423A ALA 3.6 5.2 - - - +
1424A ARG 3.1 0.4 - - - -
1425A GLU* 1.3 75.8 - - - +
1427A GLN* 1.3 69.0 + - - +
1428A PHE* 3.5 17.5 - - + -
1451A LEU* 4.3 9.4 - - + -
1455A TRP* 4.2 22.9 - - + +
1458A ARG* 2.9 27.2 + - - +
1467A ASN* 4.1 14.8 - - + +
1468A LEU* 3.8 20.9 - - + -
1471A ALA* 3.8 21.1 - - + -
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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
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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