Contacts of the helix formed by residues 874 - 883 (chain A) in PDB entry 4KXA
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 ASN 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A LYS* 2.9 29.1 - - - +
870A TRP* 2.9 65.8 + - + +
871A ILE 3.7 2.9 - - - -
873A LEU* 1.3 88.5 + - - +
875A TRP* 1.3 64.6 + - - +
876A ASP 3.4 2.7 - - - -
877A TYR* 3.3 13.2 + - + +
878A LEU* 3.0 24.0 + - - +
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Residues in contact with TRP 875 (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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871A ILE* 3.0 31.1 + - + +
872A GLN 3.4 11.4 + - - +
873A LEU 3.5 0.8 + - - -
874A ASN* 1.3 78.0 - - - +
876A ASP* 1.3 65.1 + - - +
878A LEU* 3.1 10.6 + - + +
879A VAL* 2.9 50.2 + - + +
884A LEU* 4.8 11.1 - - + +
889A LEU* 3.6 39.9 - - + -
890A GLY* 5.6 2.0 - - - -
892A ILE* 4.0 16.4 - - + -
893A VAL* 4.7 11.2 - - + -
911A PHE* 3.8 20.4 - + + -
915A TYR* 3.5 43.1 - + + +
917A GLN 5.1 2.0 + - - -
918A ALA 5.7 2.2 - - - -
925A ARG* 3.9 20.3 - - - +
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Residues in contact with ASP 876 (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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873A LEU 5.3 1.0 + - - +
874A ASN 3.4 0.2 - - - -
875A TRP* 1.3 77.9 - - - +
877A TYR* 1.3 57.0 + - - +
879A VAL* 3.4 7.0 + - - +
880A ASN* 2.9 31.8 + - - +
915A TYR* 3.4 33.5 + - - -
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Residues in contact with TYR 877 (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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839A LEU 5.2 0.4 - - - -
840A LYS* 3.6 60.1 + - + +
842A THR* 5.6 0.5 - - - +
870A TRP* 4.8 3.8 - + - -
874A ASN* 3.3 15.5 + - + +
875A TRP 3.2 0.4 - - - -
876A ASP* 1.3 78.3 - - - +
878A LEU* 1.3 78.3 + - + +
880A ASN* 3.8 7.7 + - - +
881A ARG* 2.8 76.5 + - + +
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Residues in contact with LEU 878 (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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850A VAL* 4.6 7.2 - - + -
851A PHE* 4.6 12.3 - - + -
854A ILE* 4.8 0.2 - - + -
870A TRP* 3.9 29.8 - - + -
871A ILE* 4.3 24.2 - - + -
874A ASN 3.0 17.0 + - - +
875A TRP* 3.1 12.5 + - + +
877A TYR* 1.3 92.3 - - + +
879A VAL* 1.3 60.3 + - - +
881A ARG* 3.3 0.9 + - - -
882A TYR* 2.8 55.9 + - + +
889A LEU* 3.8 25.6 - - + -
892A ILE* 5.5 0.2 - - + -
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Residues in contact with VAL 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A TRP* 2.9 53.6 + - + +
876A ASP* 3.7 7.2 - - - +
878A LEU* 1.3 76.7 - - - +
880A ASN* 1.3 57.1 + - - +
883A THR* 2.6 34.6 + - - +
884A LEU* 3.9 38.6 - - + +
889A LEU* 3.9 9.2 - - + -
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Residues in contact with ASN 880 (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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876A ASP 2.9 18.4 + - - +
877A TYR* 3.8 8.5 + - - +
879A VAL* 1.3 79.8 - - - +
881A ARG* 1.3 63.4 + - - +
883A THR* 4.4 6.9 + - - +
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Residues in contact with ARG 881 (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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198A GLY 4.1 15.3 - - - +
199A SER* 5.7 0.5 - - - -
839A LEU 3.0 22.8 + - - -
840A LYS* 4.3 1.6 - - - +
842A THR* 3.4 23.9 - - - +
845A ILE 4.5 2.2 + - - -
847A THR* 3.1 40.1 + - + +
850A VAL* 3.9 11.3 - - - +
877A TYR* 2.8 63.2 + - + +
878A LEU* 3.8 3.6 - - - +
880A ASN* 1.3 80.4 - - - +
882A TYR* 1.3 88.7 + - + +
883A THR* 5.3 1.3 - - - +
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Residues in contact with TYR 882 (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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200A LEU* 5.7 0.9 - - + -
847A THR* 2.7 49.7 + - + +
850A VAL* 3.2 23.0 - - + +
851A PHE* 3.7 35.4 - + - -
878A LEU* 2.8 34.9 + - + +
881A ARG* 1.3 97.2 + - + +
883A THR* 1.3 79.1 + - - +
886A ASN* 3.4 38.8 + - + +
889A LEU* 4.1 8.5 - - + -
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Residues in contact with THR 883 (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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138A GLU* 5.2 10.1 - - - +
879A VAL* 2.6 26.2 + - - +
880A ASN 4.9 6.1 - - - +
881A ARG 5.3 1.3 - - - +
882A TYR* 1.3 82.6 + - - +
884A LEU* 1.3 59.6 + - - +
885A ASN* 3.0 19.2 + - - +
886A ASN* 3.0 23.6 + - - +
889A LEU* 3.6 10.4 - - - +
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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