Contacts of the strand formed by residues 874 - 880 (chain A) in PDB entry 1KLN
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 874 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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699A TYR* 4.8 0.6 - - - -
866A TRP* 4.5 1.8 - - + -
867A LEU* 3.5 37.0 - - + +
872A PRO* 2.7 31.2 + - + +
873A ARG* 1.3 76.0 - - - +
875A ARG* 1.3 63.0 + - - +
886A PHE* 3.9 30.5 - - + -
887A GLU 3.2 7.2 - - - +
888A VAL* 3.8 22.2 - - + -
896A VAL* 4.0 19.5 - - + -
900A ILE* 5.7 0.2 - - + -
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Residues in contact with ARG 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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543A ASN* 3.7 37.8 - - - +
654A ARG* 2.9 36.0 - - - +
696A PRO* 5.1 2.6 - - - +
699A TYR* 6.0 2.5 - - + -
867A LEU* 5.6 0.9 - - - -
874A VAL* 1.3 76.7 - - - +
876A MET* 1.3 59.5 + - - +
877A ILE* 3.2 9.1 + - + -
886A PHE* 3.3 1.6 - - - -
887A GLU* 2.8 64.5 + - + +
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Residues in contact with MET 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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536A VAL* 4.5 6.7 - - + +
539A ARG* 6.2 0.2 - - + -
540A ILE* 3.5 48.1 - - + +
543A ASN* 3.7 14.7 + - - +
860A MET* 4.2 16.2 - - + +
863A VAL* 4.9 3.6 - - - -
864A ASP* 4.1 34.1 - - + +
867A LEU* 4.9 11.4 - - + +
874A VAL* 5.1 0.2 - - - +
875A ARG* 1.3 68.5 - - - +
877A ILE* 1.3 60.5 + - - +
878A MET 4.8 6.5 - - - +
879A GLN* 6.3 0.2 - - - -
884A LEU* 4.0 28.0 - - + -
885A VAL 3.6 9.2 - - - +
886A PHE* 3.9 23.7 - - + -
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Residues in contact with ILE 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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540A ILE* 3.8 13.4 - - - +
543A ASN* 4.7 5.4 - - + -
544A GLY* 3.3 34.3 - - - +
545A VAL* 3.9 12.9 - - + +
654A ARG* 4.4 0.9 - - - +
657A THR* 4.8 4.7 - - - +
659A TYR* 4.5 0.5 + - - -
694A ILE 5.7 0.4 - - - +
701A ILE* 3.8 22.2 - - + -
875A ARG* 3.2 19.0 + - + +
876A MET* 1.3 75.3 - - - +
878A MET* 1.3 82.9 + - + +
885A VAL* 2.9 34.9 + - + +
886A PHE 4.2 3.6 - - - +
887A GLU* 3.5 26.0 - - + +
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Residues in contact with MET 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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540A ILE* 4.2 5.4 - - - +
545A VAL* 3.5 34.3 - - + -
657A THR* 5.0 2.2 - - + -
659A TYR* 3.2 13.9 - - - +
676A LEU* 3.8 18.6 - - + -
693A PHE* 3.8 12.8 - - + -
701A ILE* 6.0 0.4 - - + -
876A MET* 3.7 6.3 - - - +
877A ILE* 1.3 94.5 - - + +
879A GLN* 1.3 62.4 + - - +
880A VAL* 4.9 2.2 - - + -
884A LEU* 3.8 2.6 - - - +
885A VAL* 2.9 49.6 + - + +
924A TRP* 3.7 41.1 - - + -
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Residues in contact with GLN 879 (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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537A LEU* 6.5 0.2 - - + -
540A ILE* 5.0 5.8 - - + -
659A TYR* 2.9 36.4 + - + -
669A LEU* 3.7 28.9 + - - +
671A SER* 4.0 3.9 + - - -
676A LEU* 4.9 0.3 - - - +
677A GLN* 4.8 2.7 + - - +
856A ILE* 4.5 9.3 - - + +
860A MET* 3.6 41.0 - - + +
876A MET* 6.3 0.2 - - + -
878A MET* 1.3 75.6 - - - +
880A VAL* 1.3 79.1 + - - +
881A HIS* 4.1 2.3 + - - -
882A ASP 4.4 5.9 + - - -
883A GLU 3.7 11.4 - - - +
884A LEU* 4.7 10.1 - - + -
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Residues in contact with VAL 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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676A LEU* 3.7 15.5 - - + +
677A GLN* 3.6 30.1 - - + +
878A MET* 4.9 4.9 - - + -
879A GLN* 1.3 85.1 - - - +
881A HIS* 1.3 80.1 + - + +
882A ASP 2.6 19.1 + - - -
883A GLU* 3.0 34.3 + - + +
885A VAL* 5.3 0.4 - - + -
924A TRP* 3.6 31.6 - - + -
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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