Contacts of the strand formed by residues 1502 - 1506 (chain H) in PDB entry 5TWV
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 ILE1502 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343H GLY* 6.1 1.3 - - - -
1392H PHE* 3.9 30.8 - - + -
1422H LEU* 5.6 0.2 - - - -
1423H SER 4.2 6.9 + - - +
1500H THR* 3.3 20.6 - - - -
1501H SER* 1.3 86.5 + - - +
1503H PHE* 1.3 62.1 + - - +
1531H ARG* 5.6 2.5 - - - -
1532H THR* 3.4 20.2 - - - +
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Residues in contact with PHE1503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1392H PHE* 5.1 3.2 - - - -
1423H SER* 4.7 2.7 - - - -
1495H ALA* 6.1 5.2 - - + -
1500H THR* 6.0 0.7 - - - -
1502H ILE* 1.3 76.1 - - - +
1504H ILE* 1.3 58.7 + - - +
1505H MET* 5.5 2.7 - - + +
1527H ALA* 5.8 11.9 - - + +
1528H PHE* 6.2 1.1 - - - -
1531H ARG* 5.8 4.9 - - + +
1532H THR 2.7 15.0 + - - +
1533H VAL* 4.6 7.9 - - + -
1534H VAL* 2.7 34.7 + - - +
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Residues in contact with ILE1504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1389H SER* 6.2 4.0 - - - -
1392H PHE* 4.1 27.8 - - + -
1393H PHE* 5.9 4.0 - - + -
1423H SER 4.2 8.2 + - - +
1424H ILE* 4.3 5.9 - - + +
1425H ILE* 2.9 27.9 + - - +
1503H PHE* 1.3 75.2 - - - +
1505H MET* 1.3 60.7 + - - +
1534H VAL* 3.5 13.0 - - + +
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Residues in contact with MET1505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425H ILE* 3.3 8.1 - - + +
1503H PHE* 5.7 3.1 - - + -
1504H ILE* 1.3 73.0 - - - +
1506H ASP* 1.3 61.2 + - - +
1507H GLU* 3.8 1.0 + - - -
1524H VAL* 6.5 1.1 - - + -
1534H VAL 2.9 10.9 + - - +
1535H THR* 3.8 5.9 - - - -
1536H ILE* 3.1 28.0 + - - +
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Residues in contact with ASP1506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1425H ILE 3.7 7.1 + - - -
1426H LEU* 3.7 14.2 - - + +
1427H GLN* 3.3 35.4 + - + +
1504H ILE 4.3 0.4 - - - -
1505H MET* 1.3 72.0 - - - +
1507H GLU* 1.3 67.3 + - - +
1508H ALA 3.5 0.9 + - - -
1536H ILE* 4.7 8.7 - - + -
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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