Contacts of the strand formed by residues 1671 - 1676 (chain A) in PDB entry 4C8D
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 TRP1671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1386A CYS* 4.2 7.4 - - + -
1389A ARG* 3.0 52.1 + - + +
1390A LEU* 4.0 19.7 - - + +
1412A GLY 4.2 4.5 - - - -
1413A GLN* 4.1 24.0 - - + +
1414A PRO* 3.5 37.0 - - + +
1614A TRP 3.5 1.2 - - - +
1615A HIS* 3.4 6.5 - - - -
1616A ILE* 2.8 53.6 + - + +
1617A TYR* 4.0 2.5 - - - -
1618A ALA* 3.6 35.0 - - + -
1669A GLN 5.1 3.8 - - - -
1670A GLY* 1.3 76.8 - - - -
1672A ALA* 1.3 60.0 + - - +
1673A ILE* 3.6 22.3 + - + +
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Residues in contact with ALA1672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1386A CYS* 3.2 21.5 - - - -
1389A ARG* 5.2 0.4 - - - +
1593A GLY 3.4 25.1 - - - +
1594A ASP* 3.7 22.4 - - + +
1595A ALA* 4.3 9.1 - - - +
1596A ASP* 4.9 2.4 + - - +
1599A THR* 5.3 2.4 + - - +
1613A LEU* 5.0 3.6 - - + -
1614A TRP 3.4 6.1 - - - +
1615A HIS* 3.9 10.3 - - + +
1670A GLY 4.0 2.4 + - - -
1671A TRP* 1.3 69.8 - - - +
1673A ILE* 1.3 58.3 + - - +
1674A VAL 4.4 0.3 + - - -
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Residues in contact with ILE1673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385A LEU* 6.2 0.9 - - + -
1386A CYS* 4.4 0.7 - - - -
1390A LEU* 3.8 33.2 - - + -
1414A PRO* 4.5 4.0 - - + -
1415A VAL 6.2 0.4 - - - -
1416A LEU* 3.7 29.2 - - + -
1599A THR* 6.0 0.4 - - - -
1612A ALA 3.7 0.5 - - - +
1613A LEU* 3.5 2.2 - - - +
1614A TRP* 2.6 51.4 + - + +
1616A ILE* 3.8 28.9 - - + -
1671A TRP* 3.9 21.1 - - + +
1672A ALA* 1.3 78.5 - - - +
1674A VAL* 1.3 68.9 + - - +
1675A GLN 4.5 1.3 - - - +
1681A VAL* 4.6 13.9 - - + -
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Residues in contact with VAL1674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1385A LEU* 6.0 0.9 - - - +
1416A LEU* 4.5 1.4 - - - +
1590A ILE* 4.0 24.9 - - + -
1595A ALA* 4.2 4.0 - - + -
1599A THR* 3.8 28.8 + - + +
1602A ARG* 4.2 3.8 + - - -
1610A PRO* 4.1 18.6 - - + -
1612A ALA 3.3 8.7 - - - +
1613A LEU* 3.9 20.6 - - + -
1673A ILE* 1.3 82.7 - - - +
1675A GLN* 1.3 60.3 + - - +
1676A PHE* 3.4 38.2 + - + -
1679A ASP* 3.8 3.8 - - - +
1694A LEU* 4.5 4.3 - - + -
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Residues in contact with GLN1675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1416A LEU* 5.0 0.7 - - - -
1568A ASN* 3.0 38.0 + - - -
1570A MET* 3.5 31.4 - - + +
1611A GLY* 2.9 24.3 + - - -
1612A ALA 2.7 16.4 + - - +
1614A TRP* 2.7 42.9 + - + +
1673A ILE* 3.7 2.4 + - - -
1674A VAL* 1.3 70.5 - - - +
1676A PHE* 1.3 59.3 + - - +
1679A ASP* 3.0 31.1 + - + +
1681A VAL* 3.7 15.3 - - + +
1699A LYS* 3.6 5.7 - - - +
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Residues in contact with PHE1676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570A MET* 3.5 9.2 - - - +
1590A ILE* 6.0 0.2 - - + -
1599A THR* 3.7 13.9 - - + -
1602A ARG* 3.3 57.4 - - + +
1603A ILE* 3.6 28.5 - - + -
1608A GLU* 3.3 35.4 - - + +
1609A LYS 3.4 18.4 - - - +
1610A PRO* 3.6 7.9 - - + -
1611A GLY 4.0 0.4 - - - +
1674A VAL* 3.4 33.0 - - + -
1675A GLN* 1.3 75.5 - - - +
1677A LEU* 1.3 67.4 + - - +
1678A GLY 3.1 0.7 + - - -
1679A ASP* 2.9 29.2 + - - +
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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