Contacts of the strand formed by residues 1400 - 1405 (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 GLU1400 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1349H ASN 3.7 4.5 - - - +
1350H LEU* 3.4 0.5 - - - -
1351H SER* 3.0 36.4 + - - +
1398H MET* 3.3 8.0 - - - +
1399H PHE* 1.3 78.1 - - + +
1401H GLY* 1.3 69.2 + - - +
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Residues in contact with GLY1401 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1348H GLN 3.4 5.6 - - - -
1349H ASN* 3.3 18.8 + - - -
1398H MET* 4.3 5.4 - - - +
1400H GLU* 1.3 80.6 - - - +
1402H ARG* 1.3 64.5 + - - +
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Residues in contact with ARG1402 (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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1346H GLN 4.6 0.2 - - - +
1347H ILE* 4.0 3.8 - - - +
1348H GLN* 3.1 37.5 + - + +
1350H LEU* 4.3 6.5 - - - +
1398H MET* 5.1 3.8 - - - -
1400H GLU 4.1 0.2 + - - -
1401H GLY* 1.3 76.5 - - - +
1403H ILE* 1.3 62.4 + - - +
1404H ILE* 4.2 1.9 + - + -
1409H ASP* 5.0 13.0 - - + -
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Residues in contact with ILE1403 (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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1347H ILE* 3.7 23.6 - - + -
1350H LEU* 5.5 3.8 - - + -
1391H ALA* 5.5 11.7 - - + +
1398H MET* 5.6 4.6 - - + +
1402H ARG* 1.3 75.2 - - - +
1404H ILE* 1.3 60.1 + - - +
1409H ASP* 3.4 4.0 - - - +
1410H ILE* 2.9 36.4 + - + +
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Residues in contact with ILE1404 (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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1345H ILE* 3.9 6.7 - - - +
1346H GLN* 3.2 38.1 + - + +
1347H ILE* 4.6 3.2 - - - +
1402H ARG* 4.2 1.7 - - + -
1403H ILE* 1.3 73.5 - - - +
1405H ILE* 1.3 59.3 - - - +
1406H ASP 4.2 0.2 - - - -
1407H GLY* 4.2 11.0 - - - +
1408H ILE 3.3 22.4 - - - +
1409H ASP* 4.3 2.0 - - - +
1410H ILE* 5.8 0.2 - - - -
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Residues in contact with ILE1405 (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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1344H LYS 4.3 1.1 - - - -
1345H ILE* 5.1 3.6 - - + +
1392H PHE* 6.4 2.0 - - + -
1403H ILE 4.2 0.4 + - - -
1404H ILE* 1.3 73.2 - - - +
1406H ASP* 1.3 66.4 + - + +
1407H GLY 3.1 1.3 - - - -
1408H ILE* 2.8 31.6 + - - +
1410H ILE* 5.0 8.5 - - + +
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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