Contacts of the strand formed by residues 1501 - 1504 (chain H) 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 ILE1501 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339H PRO* 4.3 27.6 - - + +
1341H GLN 4.1 5.4 - - - +
1342H GLY* 3.6 29.4 - - - +
1344H ILE* 5.5 11.0 - - + -
1404H ILE* 5.4 7.4 - - + -
1420H ARG 4.7 2.5 - - - +
1421H LEU* 3.6 35.9 - - + -
1422H SER 4.4 4.9 + - - -
1499H THR* 3.5 11.0 - - - -
1500H SER* 1.3 88.1 - - - +
1502H PHE* 1.3 66.6 + - - +
1531H THR* 3.0 27.1 - - + +
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Residues in contact with PHE1502 (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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1391H PHE* 6.0 1.8 - - - -
1421H LEU* 5.8 1.6 - - - -
1422H SER* 3.5 36.3 - - - +
1423H ILE* 5.1 0.7 - - - -
1424H ILE* 4.9 3.1 - - + -
1494H ALA* 5.6 4.0 - - + -
1495H PHE* 4.3 8.5 - + - -
1497H ARG 5.9 0.7 - - - -
1499H THR* 4.0 22.9 - - - -
1501H ILE* 1.3 79.3 - - - +
1503H ILE* 1.3 82.7 + - - +
1504H MET* 3.5 29.8 - - + -
1527H PHE* 3.5 36.1 - + - -
1530H ARG* 4.8 2.0 - - + -
1531H THR 3.1 4.7 + - - +
1532H VAL* 3.3 32.2 - - + -
1533H VAL* 2.9 25.6 + - - +
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Residues in contact with ILE1503 (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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1376H ILE* 5.5 0.9 - - + -
1387H PHE* 5.3 3.1 - - + -
1388H SER* 3.6 37.7 - - - +
1391H PHE* 3.8 26.0 - - + -
1392H PHE* 5.5 2.0 - - + -
1422H SER 3.7 8.0 + - - +
1423H ILE* 3.2 30.8 - - + -
1424H ILE 3.1 19.1 + - - -
1502H PHE* 1.3 83.5 - - - +
1504H MET* 1.3 82.1 + - - +
1532H VAL* 4.5 0.2 - - - -
1533H VAL* 3.2 37.5 - - + +
1535H ILE* 5.1 4.7 - - + -
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Residues in contact with MET1504 (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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1388H SER* 5.2 0.7 - - - -
1424H ILE* 3.6 25.6 - - + +
1491H LEU* 5.6 2.2 - - - -
1495H PHE* 3.6 28.5 - - + -
1502H PHE* 3.5 27.4 - - + -
1503H ILE* 1.3 84.6 - - - +
1505H ASP* 1.3 59.5 + - - +
1506H GLU 3.6 1.1 - - - +
1507H ALA* 4.4 15.7 - - + +
1519H LEU* 6.0 2.9 - - + -
1520H GLN* 5.4 7.9 - - - -
1523H VAL* 4.2 16.2 - - + -
1532H VAL* 4.2 13.0 - - + -
1533H VAL 3.0 8.5 + - - +
1534H THR* 4.9 9.0 - - - -
1535H ILE* 2.9 35.3 + - - +
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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