Contacts of the strand formed by residues 1531 - 1535 (chain G) in PDB entry 6C3P
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 THR1531 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341G GLN 4.3 3.1 + - - -
1342G GLY 4.5 7.0 - - - +
1344G ILE* 5.6 2.9 - - + -
1368G ILE* 4.8 9.2 - - + -
1369G ALA 4.1 7.9 - - - +
1370G PRO* 2.2 47.5 + - + +
1371G GLY 4.1 5.4 - - - +
1372G GLN 3.4 3.6 - - - -
1374G ILE* 5.8 0.4 - - + -
1500G SER 2.3 19.4 + - - -
1501G ILE* 3.0 45.9 - - + +
1502G PHE 3.1 5.2 + - - +
1529G ASP 3.6 3.0 + - - -
1530G ARG* 1.3 66.4 - - - +
1532G VAL* 1.3 64.7 + - - +
1533G VAL* 5.4 5.7 - - + +
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Residues in contact with VAL1532 (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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1371G GLY 4.8 0.3 - - - +
1372G GLN 3.1 10.7 + - - +
1373G LYS* 3.7 5.9 - - + -
1374G ILE* 3.4 26.3 + - - +
1502G PHE* 3.3 51.6 - - + +
1504G MET* 4.2 12.1 - - + -
1523G VAL* 5.6 1.8 - - + -
1524G MET* 6.2 3.4 - - + -
1527G PHE* 4.4 13.7 - - + +
1530G ARG* 4.4 8.1 - - + +
1531G THR* 1.3 79.1 - - - +
1533G VAL* 1.3 75.5 + - - +
1534G THR* 4.1 14.3 - - + +
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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
----------------------------------------------------------
1344G ILE* 5.3 7.6 - - + -
1368G ILE* 4.9 9.6 - - + -
1374G ILE* 3.7 24.9 - - + -
1376G ILE* 3.7 30.5 - - + -
1387G PHE* 5.4 0.4 - - + -
1391G PHE* 4.5 18.4 - - + -
1502G PHE 2.9 11.6 + - - +
1503G ILE* 3.2 27.4 - - + +
1504G MET 3.0 26.0 + - - -
1531G THR* 5.4 6.5 - - + +
1532G VAL* 1.3 78.6 - - - +
1534G THR* 1.3 64.7 + - - +
1535G ILE* 5.7 0.2 - - + -
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Residues in contact with THR1534 (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 LYS* 5.4 1.1 - - + -
1374G ILE 2.8 24.1 + - - +
1375G GLY* 3.2 7.8 - - - -
1376G ILE* 2.8 28.4 + - - +
1504G MET* 4.3 10.8 - - - +
1520G GLN* 4.9 11.7 - - - +
1524G MET* 4.6 19.7 - - + -
1532G VAL* 4.1 18.4 - - + +
1533G VAL* 1.3 78.6 - - - +
1535G ILE* 1.3 66.0 + - - +
1536G ALA* 3.9 3.7 + - - +
1541G THR* 6.2 2.0 - - - -
1542G ILE* 4.6 7.2 - - - +
1545G ALA* 4.6 4.2 - - - +
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Residues in contact with ILE1535 (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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1376G ILE* 3.4 35.4 - - + +
1384G LYS* 3.6 52.0 - - + +
1388G SER* 4.9 7.6 - - - -
1503G ILE* 5.1 4.9 - - + -
1504G MET* 2.9 27.7 + - - +
1505G ASP* 3.5 18.8 - - - +
1506G GLU* 3.1 39.1 + - + +
1507G ALA 4.2 1.4 + - - -
1534G THR* 1.3 76.6 - - - +
1536G ALA* 1.3 64.6 + - - +
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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