Contacts of the helix formed by residues 957 - 967 (chain D) 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 VAL 957 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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953D ARG 4.7 0.9 - - - -
954D LEU 4.5 0.4 - - - -
955D ASP 3.5 0.4 + - - -
956D LEU* 1.3 68.1 - - - +
958D HIS* 1.3 58.1 + - - +
959D THR 3.3 2.5 - - - +
960D ALA* 3.7 10.3 - - - +
961D ALA* 2.9 22.5 + - - -
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Residues in contact with HIS 958 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954D LEU 3.6 8.9 + - - -
955D ASP* 3.0 8.0 + - - +
956D LEU 2.9 8.3 + - - -
957D VAL* 1.3 76.8 - - - +
959D THR* 1.3 58.5 + - - +
961D ALA* 3.3 1.8 + - - +
962D LEU* 2.9 23.7 + - - -
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Residues in contact with THR 959 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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955D ASP 3.5 8.1 + - - -
957D VAL 4.2 1.2 - - - +
958D HIS* 1.3 75.4 - - - +
960D ALA* 1.3 58.5 + - - +
962D LEU* 3.3 2.2 + - - +
963D MET* 2.9 26.2 + - - -
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Residues in contact with ALA 960 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897D LEU 5.4 1.6 - - - -
898D PRO* 4.3 26.5 - - - +
957D VAL* 3.5 14.1 + - - +
958D HIS 3.3 0.4 - - - -
959D THR* 1.3 77.6 - - - +
961D ALA* 1.3 61.5 + - - +
963D MET* 3.2 2.4 + - - +
964D LEU* 2.9 21.7 + - - -
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Residues in contact with ALA 961 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957D VAL 2.9 16.4 + - - -
958D HIS* 3.6 4.7 - - - +
959D THR 3.2 0.2 - - - -
960D ALA* 1.3 76.1 - - - +
962D LEU* 1.3 55.8 + - - +
964D LEU* 3.3 2.9 + - - +
965D ASP* 2.9 25.1 + - - -
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Residues in contact with LEU 962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958D HIS 2.9 14.2 + - - -
959D THR* 3.3 4.2 + - - +
960D ALA 3.3 0.2 - - - -
961D ALA* 1.3 76.4 - - - +
963D MET* 1.3 56.8 + - - +
965D ASP* 3.2 1.8 + - - +
966D LYS* 2.9 27.2 + - - -
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Residues in contact with MET 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959D THR 2.9 15.1 + - - -
960D ALA* 3.2 3.5 + - - +
962D LEU* 1.3 76.4 - - - +
964D LEU* 1.3 62.2 + - - +
966D LYS* 3.4 1.1 + - - +
967D ASN* 3.2 19.6 + - - -
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Residues in contact with LEU 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898D PRO 6.1 1.1 - - - -
960D ALA 2.9 14.5 + - - -
961D ALA* 3.7 2.9 - - - +
963D MET* 1.3 77.0 - - - +
965D ASP* 1.3 59.9 + - - +
967D ASN* 3.7 1.2 + - - +
968D ASN 3.1 2.4 + - - -
969D LEU* 2.8 33.6 + - - +
970D VAL* 3.3 8.4 + - - +
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Residues in contact with ASP 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961D ALA 2.9 15.4 + - - -
962D LEU* 3.2 4.0 + - - +
964D LEU* 1.3 76.7 - - - +
966D LYS* 1.3 63.2 + - - +
968D ASN* 3.1 13.0 + - - -
970D VAL 3.3 18.8 - - - +
972D TYR 5.7 2.2 - - - +
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Residues in contact with LYS 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962D LEU 2.9 15.3 + - - -
963D MET* 3.9 2.2 - - - +
964D LEU 3.4 0.2 - - - -
965D ASP* 1.3 77.1 - - - +
967D ASN* 1.3 57.6 - - - +
968D ASN 3.3 1.2 + - - -
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Residues in contact with ASN 967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963D MET 3.2 13.8 + - - -
964D LEU* 3.8 0.7 - - - +
966D LYS* 1.3 77.3 - - - +
968D ASN* 1.3 63.5 + - - +
969D LEU* 3.3 3.6 + - - -
995D ASN 4.8 12.5 - - - +
998D VAL 5.4 0.7 - - - -
999D GLN* 4.4 20.7 + - - +
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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