Contacts of the strand formed by residues 1548 - 1551 (chain E) 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 VAL1548 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1375E GLY 3.2 3.6 - - - -
1377E CYS* 4.2 5.4 - - - -
1542E ILE* 4.0 34.5 - - + +
1545E ALA 5.1 0.2 - - - +
1547E LEU* 1.3 74.5 - - - +
1549E ILE* 1.3 62.9 + - - +
1550E VAL* 4.1 20.4 + - + -
1559E PHE* 3.0 6.4 - - - +
1560E ASP 2.6 36.8 + - - +
1562E PRO* 3.6 36.6 - - + -
1565E LEU* 3.9 12.8 - - + +
1573E PHE* 4.6 13.5 - - + -
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Residues in contact with ILE1549 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1366E ALA* 5.4 6.1 - - + -
1368E ILE* 4.9 12.3 - - + -
1374E ILE* 3.8 22.9 - - + -
1375E GLY 2.4 17.3 + - - +
1376E ILE* 3.2 37.4 - - + +
1377E CYS* 2.8 32.9 + - - +
1387E PHE* 6.1 0.7 - - + -
1547E LEU* 5.1 5.2 - - + -
1548E VAL* 1.3 78.0 - - - +
1550E VAL* 1.3 61.6 + - - +
1551E LEU* 4.7 2.7 - - + -
1556E ILE* 3.7 33.0 - - + -
1559E PHE* 3.7 22.0 - - + -
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Residues in contact with VAL1550 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377E CYS* 3.8 16.4 - - - +
1378E GLY* 5.2 1.1 - - - -
1548E VAL* 4.1 11.8 + - + +
1549E ILE* 1.3 77.9 - - - +
1551E LEU* 1.3 69.2 + - - +
1552E LYS* 4.1 2.6 + - + +
1556E ILE* 3.0 10.3 - - - +
1557E LEU* 2.8 51.4 + - + +
1558E GLU 5.4 0.4 - - - +
1559E PHE* 4.8 0.6 - - - +
1565E LEU* 5.0 4.9 - - + -
1571E SER* 4.4 11.0 - - - +
1572E VAL* 5.5 4.9 - - + -
1573E PHE* 4.0 25.8 - - + +
1576E PHE* 4.6 18.6 - - + -
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Residues in contact with LEU1551 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361E LEU* 4.4 13.0 - - + -
1364E VAL* 5.5 1.1 - - + -
1376E ILE* 4.1 18.6 - - + -
1377E CYS 3.4 8.5 + - - +
1378E GLY* 4.1 7.8 - - - -
1379E ARG* 3.9 6.6 + - - -
1382E SER* 2.9 31.9 + - - +
1383E GLY 4.2 6.1 - - - +
1384E LYS* 3.7 39.0 - - + +
1387E PHE* 5.0 8.3 - - + -
1549E ILE* 4.7 1.6 - - + -
1550E VAL* 1.3 76.6 - - - +
1552E LYS* 1.3 60.5 + - - +
1555E ALA* 3.3 28.3 - - - +
1556E ILE* 3.6 19.7 - - + -
1576E PHE* 6.0 0.2 - - - -
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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