Contacts of the helix formed by residues 940 - 947 (chain D) in PDB entry 3KKA
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 THR 940 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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938D GLN 5.0 3.8 - - - +
939D MET* 1.3 76.7 - - - +
941D ASN* 1.3 64.7 + - - +
942D ASP* 3.2 24.8 - - - +
943D ASP* 2.9 28.9 + - - +
944D ILE* 3.3 15.7 + - - +
962D LEU* 4.8 2.2 - - - -
966D LYS* 4.4 4.7 - - - +
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Residues in contact with ASN 941 (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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940D THR* 1.3 73.4 - - - +
942D ASP* 1.3 61.9 + - - +
944D ILE* 3.1 28.0 + - + +
945D LYS* 3.3 7.8 + - - +
959D ALA* 3.2 32.6 - - + +
962D LEU* 5.3 3.5 - - - +
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Residues in contact with ASP 942 (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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940D THR* 3.2 14.8 - - - +
941D ASN* 1.3 78.3 - - - +
943D ASP* 1.3 59.1 + - - +
945D LYS* 3.6 7.3 + - - +
946D ARG* 3.0 35.5 + - - +
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Residues in contact with ASP 943 (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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930D TYR* 3.6 17.0 + - + +
938D GLN* 4.6 3.3 - - - +
939D MET* 3.5 27.4 - - + +
940D THR* 2.9 37.0 + - - +
942D ASP* 1.3 77.2 - - - +
944D ILE* 1.3 65.1 + - - +
946D ARG* 3.2 13.2 + - + +
947D ILE* 3.0 27.8 + - + +
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Residues in contact with ILE 944 (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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925D PHE* 5.5 1.1 - - + -
939D MET* 4.2 16.6 - - + -
940D THR 3.8 6.5 - - - +
941D ASN* 3.1 23.9 + - - +
943D ASP* 1.3 77.9 - - - +
945D LYS* 1.3 62.2 + - - +
947D ILE* 3.3 12.0 - - + +
949D VAL* 3.3 44.4 + - + +
955D GLN* 4.4 16.6 - - + -
958D ILE* 4.0 23.1 - - + -
959D ALA* 3.8 31.2 - - + -
962D LEU* 4.2 15.0 - - + -
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Residues in contact with LYS 945 (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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941D ASN 3.3 7.4 + - - +
942D ASP* 3.8 9.9 - - - +
943D ASP 3.3 0.4 - - - -
944D ILE* 1.3 75.8 - - - +
946D ARG* 1.3 67.2 + - - +
948D GLY* 2.9 17.3 + - - -
949D VAL 3.6 11.6 + - - +
950D ARG* 5.4 6.0 - - + +
955D GLN* 4.0 21.1 - - - +
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Residues in contact with ARG 946 (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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942D ASP* 3.0 29.7 + - - +
943D ASP* 3.4 18.6 - - - +
945D LYS* 1.3 75.8 - - - +
947D ILE* 1.3 61.1 + - + +
948D GLY* 3.2 3.8 + - - -
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Residues in contact with ILE 947 (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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924D HIS* 3.5 36.5 - - + +
925D PHE* 3.8 58.8 - - + +
928D ALA* 3.4 27.6 - - + -
930D TYR* 3.9 15.7 - - + -
939D MET* 4.2 4.5 - - + -
943D ASP* 3.0 14.7 + - + +
944D ILE* 3.3 16.8 - - - +
946D ARG* 1.3 77.5 - - + +
948D GLY* 1.3 56.3 + - - +
949D VAL* 4.4 7.0 - - + -
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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