Contacts of the strand formed by residues 1531 - 1545 (chain G) in PDB entry 2VKZ
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 VAL1531 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1528G GLU 5.1 2.7 - - - +
1529G GLN 3.7 6.0 + - - +
1530G LYS* 1.4 83.8 - - - +
1532G ASN* 1.3 74.7 + - - +
1533G LEU* 4.5 0.6 - - + +
1630G GLY* 4.3 0.7 - - - -
1631G MET* 2.8 39.9 + - + +
1794G SER 3.6 20.6 - - - +
1795G LYS* 3.5 41.3 - - + +
1796G GLY* 4.9 1.6 - - - +
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Residues in contact with ASN1532 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530G LYS* 4.3 1.5 + - - +
1531G VAL* 1.3 89.3 - - - +
1533G LEU* 1.3 71.5 + - - +
1629G VAL* 3.7 27.0 - - - +
1630G GLY* 4.0 1.0 - - - -
1637G LEU* 5.8 1.2 - - - +
1639G LYS* 5.8 0.5 + - - -
1795G LYS* 5.7 1.0 - - - +
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Residues in contact with LEU1533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR 4.6 9.0 - - - +
90A TYR* 3.8 16.4 - - + +
91A THR* 5.4 0.7 - - - -
1531G VAL* 6.0 0.4 - - + -
1532G ASN* 1.3 87.6 - - - +
1534G GLU* 1.3 68.6 + - - +
1535G ASN* 3.8 11.2 - - - +
1536G PRO* 5.9 0.2 - - - +
1537G ILE* 3.8 16.4 - - + -
1628G HIS* 3.6 47.8 - - + +
1629G VAL 3.0 14.0 + - - +
1630G GLY* 3.4 16.6 - - - +
1631G MET* 3.7 24.5 - - + -
1797G LEU* 5.8 0.4 - - + -
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Residues in contact with GLU1534 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 4.0 33.1 + - + +
1533G LEU* 1.3 78.7 - - - +
1535G ASN* 1.3 76.6 + - - +
1536G PRO* 4.4 2.9 - - - +
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Residues in contact with ASN1535 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TYR 5.2 0.9 - - - +
91A THR* 5.4 1.4 - - - +
92A PRO* 5.2 14.7 + - + +
1533G LEU* 3.8 12.4 - - - +
1534G GLU* 1.3 94.2 + - - +
1536G PRO* 1.3 78.0 - - + +
1537G ILE* 3.3 14.4 + - - +
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Residues in contact with PRO1536 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1534G GLU 4.4 3.6 - - - +
1535G ASN* 1.3 91.5 - - + +
1537G ILE* 1.3 60.4 + - - +
1538G PRO* 3.7 8.2 - - - +
1627G GLN* 3.7 26.5 - - + +
1628G HIS 3.5 9.6 - - - +
1629G VAL* 4.7 15.7 - - + +
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Residues in contact with ILE1537 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A TYR* 3.3 33.9 - - + +
92A PRO* 4.3 23.6 - - + -
1533G LEU* 3.8 12.8 - - + -
1535G ASN 3.5 13.7 - - - +
1536G PRO* 1.3 72.5 - - - +
1538G PRO* 1.3 76.6 - - + +
1539G ILE* 3.5 1.6 + - + +
1627G GLN* 4.1 2.0 - - - -
1628G HIS* 2.7 58.3 + - + +
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Residues in contact with PRO1538 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PRO 6.1 1.3 - - - +
1536G PRO 3.7 8.3 - - - +
1537G ILE* 1.3 97.5 - - + +
1539G ILE* 1.3 61.1 - - - +
1540G ALA 5.2 0.9 - - - +
1626G ILE 4.1 5.2 - - - +
1627G GLN* 4.2 11.0 - - + -
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Residues in contact with ILE1539 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537G ILE* 3.8 9.6 - - + +
1538G PRO* 1.3 77.5 - - - +
1540G ALA* 1.3 69.6 + - + +
1596G TRP* 3.7 29.4 - - + +
1597G ALA* 4.3 4.3 - - + -
1626G ILE* 2.8 28.7 + - + +
1627G GLN 3.7 16.6 - - - -
1628G HIS* 3.8 9.9 - - + +
1636G LYS* 6.4 0.4 - - + +
1638G ILE* 3.6 31.0 - - + -
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Residues in contact with ALA1540 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538G PRO* 5.2 1.0 - - - +
1539G ILE* 1.3 90.0 - - + +
1541G VAL* 1.3 65.2 + - - +
1542G LEU* 4.1 15.9 - - + -
1596G TRP* 4.1 29.8 - - + -
1624G THR 4.2 0.3 - - - +
1625G SER* 3.6 1.4 - - - -
1626G ILE* 3.0 32.1 + - + +
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Residues in contact with VAL1541 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540G ALA* 1.3 78.3 - - - +
1542G LEU* 1.3 66.8 + - - +
1543G ASP* 5.5 1.0 - - - +
1623G LYS* 4.3 29.8 - - + +
1624G THR 3.7 7.4 - - - +
1625G SER* 3.8 19.7 - - - -
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Residues in contact with LEU1542 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540G ALA* 4.3 11.7 - - + -
1541G VAL* 1.3 81.1 - - - +
1543G ASP* 1.3 62.5 + - - +
1592G LEU* 3.5 41.5 - - + -
1596G TRP* 3.2 62.4 - - + +
1622G LEU 3.4 1.0 - - - +
1623G LYS* 3.2 5.7 - - - -
1624G THR* 2.9 37.0 + - - +
1626G ILE* 4.0 14.8 - - + -
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Residues in contact with ASP1543 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1541G VAL 5.5 0.8 - - - +
1542G LEU* 1.3 75.7 - - - +
1544G SER* 1.3 61.1 + - - +
1545G TYR* 4.6 20.9 - - + +
1592G LEU* 4.9 4.6 - - - +
1621G ALA* 6.1 1.0 - - + +
1622G LEU 3.7 1.1 - - - -
1623G LYS* 2.9 41.3 + - - +
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Residues in contact with SER1544 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543G ASP* 1.3 74.5 - - - +
1545G TYR* 1.3 82.8 + - - +
1584G PHE* 5.6 0.3 - - - -
1588G SER* 3.7 21.1 + - - -
1589G VAL* 5.5 2.2 + - - +
1592G LEU* 4.4 12.8 - - - +
1621G ALA* 3.4 1.9 - - - +
1622G LEU* 2.7 53.8 + - - +
1624G THR* 4.3 12.3 - - - -
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Residues in contact with TYR1545 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543G ASP* 4.6 21.8 - - + +
1544G SER* 1.3 99.6 + - - +
1546G THR* 1.3 67.8 + - - +
1584G PHE* 3.8 16.2 - - - -
1588G SER* 4.6 0.9 + - - -
1619G ASN* 5.7 3.6 - - - -
1620G THR 3.5 14.6 - - - +
1621G ALA* 3.6 22.6 - - + +
1622G LEU* 5.0 2.0 - - - -
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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