Contacts of the helix formed by residues 1405 - 1411 (chain A) in PDB entry 6XAF
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 HIS1405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1402A TYR* 3.0 24.8 + + + +
1403A SER 3.3 0.6 - - - -
1404A THR* 1.3 77.8 - - - +
1406A PRO* 1.3 83.8 - - + +
1407A HIS* 2.9 39.3 + - + +
1408A PHE* 2.9 26.5 + + + -
1409A MET 3.1 7.4 + - - -
1441B ARG* 3.4 23.4 - - - +
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Residues in contact with PRO1406 (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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1404A THR 3.7 5.8 - - - +
1405A HIS* 1.3 98.8 - - + +
1407A HIS* 1.3 61.8 + - - +
1409A MET* 4.4 7.2 - - + -
1410A THR* 2.9 31.7 + - + +
1406B PRO* 4.2 26.0 - - + -
1409B MET* 6.1 1.6 - - + -
1410B THR* 4.0 23.3 - - + -
1441B ARG* 4.5 13.0 - - - +
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Residues in contact with HIS1407 (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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1405A HIS* 2.9 26.0 + - + +
1406A PRO* 1.3 77.5 - - - +
1408A PHE* 1.3 86.1 + + + +
1410A THR* 3.6 2.6 + - - -
1411A GLN* 2.8 51.5 + - + +
1412A ARG* 6.0 1.6 - - + -
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Residues in contact with PHE1408 (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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1336A LYS* 3.8 15.0 - - - +
1402A TYR* 3.4 67.8 - + - -
1403A SER* 3.4 19.7 - - - +
1405A HIS* 2.9 17.0 + + + +
1407A HIS* 1.3 94.1 - + + +
1409A MET* 1.3 66.7 + - - +
1410A THR 3.1 2.1 + - - -
1412A ARG* 3.7 38.7 + - + +
1413A ALA* 4.8 0.2 - - - +
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Residues in contact with MET1409 (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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1336A LYS* 3.8 26.0 - - - +
1338A MET* 4.3 23.3 - - + +
1404A THR* 3.4 31.0 - - - +
1405A HIS 3.1 5.4 + - - +
1406A PRO* 3.5 6.7 + - + +
1408A PHE* 1.3 77.0 - - - +
1410A THR* 1.3 64.2 + - + +
1413A ALA* 4.3 8.6 - - - +
1415A TYR* 4.4 4.9 + - - -
1441A ARG* 5.1 6.6 + - - +
1393B TRP* 3.7 36.3 - - + -
1395B PHE* 6.0 0.2 - - + -
1404B THR* 4.3 24.7 - - - +
1406B PRO* 6.1 1.8 - - + -
1409B MET* 4.0 25.1 - - + -
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Residues in contact with THR1410 (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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1406A PRO* 2.9 21.9 + - + +
1407A HIS* 3.6 3.3 + - - -
1408A PHE 3.1 0.4 - - - -
1409A MET* 1.3 86.2 - - + +
1411A GLN* 1.3 64.0 + - - +
1413A ALA* 5.2 1.1 - - - -
1441A ARG* 3.2 40.8 - - - +
1442A ALA* 3.0 31.7 - - - +
1443A SER 4.8 0.2 + - - -
1445A SER* 4.0 1.0 + - - -
1406B PRO* 4.2 18.6 - - + -
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Residues in contact with GLN1411 (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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1407A HIS* 2.8 46.5 + - + +
1410A THR* 1.3 77.6 + - - +
1412A ARG* 1.3 58.5 + - + +
1413A ALA 3.0 7.4 + - - -
1444A SER* 4.7 8.7 + - - +
1445A SER* 3.8 4.7 + - - -
1511A PHE* 3.2 18.3 - - - -
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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