Contacts of the strand formed by residues 1579 - 1587 (chain B) 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 GLY1579 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1517B VAL 3.2 11.7 - - - -
1518B LEU* 3.9 2.9 - - - -
1519B LEU 3.0 18.7 - - - +
1520B PRO* 3.9 0.8 - - - +
1521B PRO* 3.6 12.1 - - - +
1557B PRO* 3.8 0.2 - - - +
1558B TYR* 2.9 32.3 + - - +
1577B VAL 3.6 1.6 - - - -
1578B ILE* 1.3 81.0 + - - +
1580B SER* 1.3 60.3 + - - -
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Residues in contact with SER1580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515B LEU 3.7 0.7 - - - +
1516B THR* 3.3 6.1 - - - +
1517B VAL* 2.6 38.0 + - - +
1519B LEU 2.3 24.2 + - - -
1520B PRO 3.3 0.9 + - - -
1521B PRO* 3.0 22.7 - - - +
1524B LEU* 4.0 7.3 - - - +
1555B VAL* 3.8 20.0 - - - -
1556B PHE 3.3 5.6 - - - -
1558B TYR* 3.7 3.6 - - - +
1579B GLY* 1.3 70.3 - - - -
1581B VAL* 1.3 62.6 + - - +
1582B VAL* 4.1 9.4 - - - -
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Residues in contact with VAL1581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1514B VAL* 3.9 24.0 - - + -
1515B LEU 3.5 3.8 - - - +
1516B THR* 4.3 10.5 - - - +
1555B VAL* 3.5 2.6 - - - -
1556B PHE* 2.7 59.1 + - + +
1557B PRO 4.8 4.3 - - - +
1558B TYR* 4.1 26.2 - - + -
1580B SER* 1.3 74.2 - - - +
1582B VAL* 1.3 62.1 + - - +
1583B MET* 4.8 7.2 - - + -
1630B ARG* 5.4 4.9 - - - +
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Residues in contact with VAL1582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513B LEU 3.6 1.4 - - - +
1514B VAL* 3.4 4.2 - - - +
1515B LEU* 2.7 50.1 + - + +
1517B VAL* 4.5 11.4 - - + -
1524B LEU* 4.0 17.0 - - + -
1531B PHE* 4.7 6.5 - - + -
1545B PHE* 3.6 31.0 - - + -
1554B MET 4.1 2.0 - - - -
1555B VAL* 4.0 20.9 - - + +
1580B SER* 4.1 9.2 - - - -
1581B VAL* 1.3 76.3 - - - +
1583B MET* 1.3 65.1 + - - +
1584B LEU* 3.8 18.8 - - + -
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Residues in contact with MET1583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512B VAL* 3.9 20.4 - - + -
1513B LEU 3.6 3.8 - - - -
1514B VAL* 4.6 15.5 - - + -
1545B PHE* 3.7 2.4 - - - -
1546B ARG* 3.1 32.5 + - + -
1554B MET* 3.3 44.4 + - + +
1556B PHE* 3.8 20.9 - - + -
1581B VAL* 4.8 10.5 - - + +
1582B VAL* 1.3 80.5 - - - +
1584B LEU* 1.3 66.5 + - - +
1630B ARG* 6.0 1.8 - - - +
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Residues in contact with LEU1584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512B VAL* 3.4 9.3 - - - +
1513B LEU* 2.8 45.5 + - + +
1515B LEU* 3.7 15.7 - - + -
1531B PHE* 4.4 6.1 - - + -
1532B LEU* 3.7 20.4 - - + -
1535B LEU* 3.6 31.9 - - + -
1543B LEU* 4.5 11.7 - - + -
1544B ARG 3.3 14.1 - - - +
1545B PHE* 3.5 29.6 - - + -
1546B ARG* 5.0 0.2 - - - -
1582B VAL* 3.8 10.1 - - + -
1583B MET* 1.3 78.1 - - - +
1585B GLU* 1.3 67.3 + - - +
1586B ILE* 5.4 0.2 - - - +
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Residues in contact with GLU1585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508B LEU* 3.8 17.6 - - + +
1511B GLY 5.2 9.6 - - - +
1512B VAL* 5.5 2.2 - - + -
1542B SER 3.8 0.3 - - - +
1543B LEU* 3.3 10.0 - - - +
1544B ARG* 2.3 79.0 + - + +
1546B ARG* 3.0 49.9 + - + +
1547B LEU 4.6 1.5 + - - -
1584B LEU* 1.3 78.5 - - - +
1586B ILE* 1.3 64.0 + - - +
1587B ASP 4.0 0.8 + - - -
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Residues in contact with ILE1586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508B LEU* 3.2 7.2 - - - +
1509B ALA* 2.9 43.6 + - + +
1511B GLY 5.5 2.0 + - - -
1513B LEU* 4.9 11.4 - - + +
1539B LEU* 5.2 1.8 - - + -
1541B THR* 3.7 19.7 - - + -
1542B SER 3.5 2.7 - - - +
1543B LEU* 3.4 19.7 - - + -
1585B GLU* 1.3 74.1 - - - +
1587B ASP* 1.3 61.0 + - - +
1588B ASN* 3.4 28.5 - - - +
1601B PHE* 4.8 5.4 - - + +
1603B ASP 4.5 3.6 - - - +
1604B ALA* 4.3 18.6 - - + -
1607B ALA* 3.8 29.8 - - + -
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Residues in contact with ASP1587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498B LEU* 3.6 16.1 - - + +
1506B ALA* 3.5 6.6 - - - +
1507B LEU 3.0 24.9 + - - -
1508B LEU* 3.7 12.3 - - + +
1541B THR* 3.3 11.7 + - - -
1542B SER* 2.8 26.6 + - - +
1544B ARG* 3.7 15.9 + - + +
1585B GLU 4.0 1.4 + - - -
1586B ILE* 1.3 71.0 - - - +
1588B ASN* 1.3 58.8 + - - +
1589B ARG* 2.8 50.8 + - - +
1590B LEU 4.9 1.2 + - - -
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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