Contacts of the helix formed by residues 1051 - 1063 (chain 1) in PDB entry 6AH0
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 SER1051 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10481 GLU 5.3 0.2 - - - -
10491 TYR 3.9 2.6 + - - -
10501 VAL* 1.3 75.3 - - - +
10521 ALA* 1.3 67.7 + - - +
10531 ARG 3.2 2.5 - - - -
10541 GLU* 3.1 14.7 + - - -
10551 TRP 3.6 4.7 + - - -
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Residues in contact with ALA1052 (chain 1).
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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10501 VAL 3.5 3.0 + - - -
10511 SER* 1.3 70.7 - - - +
10531 ARG* 1.3 54.6 + - - +
10551 TRP* 2.6 26.3 + - - +
10561 MET* 3.0 9.2 + - - -
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Residues in contact with ARG1053 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10511 SER 3.1 1.6 + - - -
10521 ALA* 1.3 73.8 - - - +
10541 GLU* 1.3 64.7 + - - +
10561 MET* 3.0 12.7 + - - +
10571 ARG* 3.1 8.8 + - - -
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Residues in contact with GLU1054 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10511 SER 3.1 9.6 + - - -
10531 ARG* 1.3 76.0 - - - +
10551 TRP* 1.3 62.3 + - - +
10571 ARG* 3.0 6.8 + - - +
10581 ILE* 2.9 15.4 + - - -
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Residues in contact with TRP1055 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10511 SER 3.6 3.8 + - - -
10521 ALA* 2.6 16.3 + - - +
10541 GLU* 1.3 69.6 - - - +
10561 MET* 1.3 54.3 + - - +
10581 ILE* 2.2 30.5 + - - +
10591 CYS 2.8 9.7 + - - -
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Residues in contact with MET1056 (chain 1).
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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10521 ALA 3.0 6.4 + - - -
10531 ARG* 3.0 8.0 + - - +
10551 TRP* 1.3 74.6 - - - +
10571 ARG* 1.3 61.4 + - - +
10591 CYS* 3.3 4.0 + - - +
10601 PHE* 3.1 19.6 + - - -
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Residues in contact with ARG1057 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10531 ARG 3.1 7.6 + - - -
10541 GLU* 3.0 9.0 + - - +
10561 MET* 1.3 77.0 - - - +
10581 ILE* 1.3 61.9 + - - +
10601 PHE* 3.3 2.5 + - - +
10611 GLU* 2.9 19.8 + - - -
5562 LYS 5.5 6.5 - - - -
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Residues in contact with ILE1058 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10541 GLU 2.9 7.7 + - - -
10551 TRP* 2.2 21.6 + - - +
10571 ARG* 1.3 68.4 - - - +
10591 CYS* 1.3 49.8 + - - +
10611 GLU* 3.0 3.3 + - - +
10621 LEU* 2.7 33.4 + - - -
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Residues in contact with CYS1059 (chain 1).
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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10551 TRP 2.8 9.9 + - - -
10561 MET* 3.3 5.3 + - - +
10581 ILE* 1.3 73.4 - - - +
10601 PHE* 1.3 57.8 + - - +
10621 LEU* 2.8 21.5 + - - +
10631 LEU* 3.1 11.8 + - - -
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Residues in contact with PHE1060 (chain 1).
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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10561 MET 3.1 13.7 + - - -
10571 ARG 3.3 3.1 + - - -
10591 CYS* 1.3 72.7 - - - +
10611 GLU* 1.3 57.6 + - - +
10631 LEU* 4.3 5.5 + - - +
10641 GLU 5.3 0.9 + - - -
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Residues in contact with GLU1061 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10571 ARG 2.9 14.0 + - - -
10581 ILE* 3.4 3.6 - - - +
10591 CYS 2.9 0.8 + - - -
10601 PHE* 1.3 76.2 - - - +
10621 LEU* 1.3 66.7 + - - +
10631 LEU 3.1 2.5 + - - -
10641 GLU* 3.7 6.2 + - - -
10651 LEU 4.2 2.3 + - - -
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Residues in contact with LEU1062 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10581 ILE 2.7 18.3 + - - -
10591 CYS* 2.8 5.8 + - - +
10611 GLU* 1.3 69.4 - - - +
10631 LEU* 1.3 51.0 + - - +
10641 GLU 2.5 0.9 + - - -
10651 LEU* 2.4 38.0 + - - +
10661 LEU 4.2 0.2 + - - -
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Residues in contact with LEU1063 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10591 CYS 3.1 11.6 + - - -
10601 PHE* 4.3 4.4 - - - +
10611 GLU 3.1 2.4 - - - -
10621 LEU* 1.3 73.3 - - - +
10641 GLU* 1.3 58.1 + - - +
10661 LEU* 3.6 11.7 + - - -
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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