Contacts of the strand formed by residues 1626 - 1632 (chain A) in PDB entry 4ZLP
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 LEU1626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1419A LEU* 3.3 44.2 - - + +
1515A LEU* 3.7 31.2 - - + -
1516A THR 3.6 15.7 - - - +
1517A VAL* 4.0 9.2 - - + +
1535A LEU* 5.5 2.5 - - + -
1611A LEU* 5.3 5.4 - - + -
1620A LEU* 4.3 13.0 - - + -
1622A PHE* 4.2 26.0 - - + -
1624A TYR 2.7 13.7 + - - +
1625A PRO* 1.3 69.2 - - - +
1627A ARG* 1.3 58.3 + - - +
1628A ASP 3.9 11.7 - - - +
1629A VAL* 4.1 7.9 - - + -
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Residues in contact with ARG1627 (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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1399A GLN* 3.2 50.2 + - - +
1419A LEU* 3.6 17.6 - - - +
1420A SER* 5.4 0.2 - - - -
1516A THR* 2.8 21.4 + - + +
1518A LEU* 4.1 36.1 - - + +
1558A TYR* 3.1 39.4 + - - -
1561A PRO* 4.4 4.8 - - - +
1578A ILE* 5.8 2.2 - - - +
1625A PRO 3.4 2.4 + - - -
1626A LEU* 1.3 74.1 - - - +
1628A ASP* 1.3 75.4 + - + +
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Residues in contact with ASP1628 (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 LEU* 3.5 7.0 - - - +
1420A SER* 3.7 24.2 - - - +
1514A VAL 4.8 0.9 - - - +
1515A LEU* 3.5 1.0 - - - -
1516A THR* 2.6 56.7 + - - +
1558A TYR* 5.1 2.4 + - - -
1626A LEU* 3.9 2.6 - - - +
1627A ARG* 1.3 92.0 - - + +
1629A VAL* 1.3 72.6 + - - +
1630A ARG* 4.3 13.8 + - - -
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Residues in contact with VAL1629 (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 LEU* 3.1 38.6 + - + +
1420A SER* 3.4 14.4 + - - -
1421A VAL* 3.9 9.5 - - + +
1513A LEU* 4.8 2.5 - - + -
1514A VAL 3.3 8.3 - - - +
1515A LEU* 4.1 18.8 - - + -
1608A ALA* 3.4 34.5 - - + +
1611A LEU* 4.1 13.0 - - + -
1626A LEU* 4.1 11.7 - - + -
1628A ASP* 1.3 80.7 - - - +
1630A ARG* 1.3 67.4 + - - +
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Residues in contact with ARG1630 (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 SER* 5.4 1.3 - - - +
1513A LEU* 3.5 3.8 - - - +
1514A VAL* 2.7 71.0 + - + +
1516A THR* 4.7 4.4 + - - -
1581A VAL* 5.2 5.5 - - - +
1583A MET* 5.7 2.8 - - - +
1605A GLN* 3.9 7.2 - - - +
1608A ALA* 3.8 13.6 - - - +
1628A ASP* 4.3 16.1 + - - -
1629A VAL* 1.3 77.5 - - - +
1631A GLY* 1.3 59.6 + - - +
1632A GLU* 2.8 34.3 + - + +
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Residues in contact with GLY1631 (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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1512A VAL 3.4 6.5 - - - -
1604A ALA* 3.7 3.6 - - - -
1605A GLN* 2.8 46.2 + - - +
1630A ARG* 1.3 75.6 - - - +
1632A GLU* 1.3 72.0 + - - +
1633A PRO* 4.6 1.4 - - - +
5010A ACT 3.7 6.8 - - - -
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Residues in contact with GLU1632 (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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1511A GLY* 3.2 4.0 - - - -
1512A VAL* 2.8 44.2 + - + +
1514A VAL* 3.9 12.3 - - + -
1630A ARG* 2.8 41.4 + - - +
1631A GLY* 1.3 78.7 - - - +
1633A PRO* 1.3 82.1 - - + +
5010A ACT 3.6 5.3 + - - -
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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