Contacts of the strand formed by residues 1532 - 1536 (chain G) in PDB entry 6BAA
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 THR1532 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343G GLY* 3.8 22.9 + - - -
1345G ILE* 5.8 6.1 - - - -
1369G ILE* 5.8 5.6 - - - -
1370G SER 5.1 2.5 - - - -
1372G GLY 4.3 2.4 - - - +
1373G GLN 3.8 5.8 - - - +
1501G SER 3.1 9.1 + - - -
1502G ILE* 3.2 20.8 - - - -
1503G PHE* 2.4 35.1 + - - +
1528G PHE* 5.5 0.2 - - - -
1531G ARG* 1.3 74.5 - - - +
1533G VAL* 1.3 54.4 - - - +
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Residues in contact with VAL1533 (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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1373G GLN 3.1 7.4 + - - +
1374G LYS* 3.7 20.4 - - + -
1375G ILE* 2.6 35.7 + - - +
1503G PHE* 3.6 11.0 - - + -
1524G VAL 5.6 0.7 - - - +
1528G PHE* 3.8 19.5 - - + -
1531G ARG 3.6 0.2 + - - -
1532G THR* 1.3 74.3 - - - +
1534G VAL* 1.3 58.8 + - - +
1535G THR* 4.0 1.6 - - - +
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Residues in contact with VAL1534 (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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1375G ILE* 3.3 7.2 - - + -
1392G PHE* 5.4 11.7 - - + -
1503G PHE* 2.6 18.5 + - - +
1504G ILE* 3.3 7.8 - - + -
1505G MET* 2.6 35.5 + - - +
1533G VAL* 1.3 72.3 - - - +
1535G THR* 1.3 56.4 + - - +
1536G ILE 3.8 0.4 + - - -
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Residues in contact with THR1535 (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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1375G ILE 2.4 23.0 + - - -
1376G GLY* 3.7 9.4 - - - -
1377G ILE* 2.5 36.2 + - - +
1505G MET* 3.5 13.5 - - - -
1533G VAL* 5.6 1.3 - - - -
1534G VAL* 1.3 72.8 - - - +
1536G ILE* 1.3 58.9 + - - +
1537G ALA* 3.2 5.6 + - - -
1543G ILE* 6.3 1.1 - - - -
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Residues in contact with ILE1536 (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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1377G ILE* 4.1 7.6 - - + -
1385G LYS* 4.6 22.7 - - + +
1389G SER* 5.3 8.7 - - - -
1505G MET 2.5 16.8 + - - +
1506G ASP* 4.4 8.3 - - + -
1507G GLU* 3.0 26.4 + - - +
1534G VAL 3.8 1.0 + - - -
1535G THR* 1.3 68.5 - - - +
1537G ALA* 1.3 62.4 + - - +
1538G HIS* 5.4 0.3 - - - +
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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