Contacts of the helix formed by residues 880 - 885 (chain A) in PDB entry 3KSY
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 SER 880 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A GLU* 3.2 40.0 - - - +
876A SER 3.0 8.1 + - - -
877A ALA 2.6 21.2 + - - -
878A MET 3.4 0.2 - - - -
879A ASN* 1.3 79.1 - - - +
881A SER* 1.3 57.2 + - - +
882A PRO* 3.7 4.3 - - - +
883A VAL* 3.4 9.5 - - - +
884A TYR* 2.7 35.5 + - - +
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Residues in contact with SER 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A ASN 3.7 1.8 + - - -
880A SER* 1.3 72.2 - - - +
882A PRO* 1.3 72.1 - - - +
883A VAL 3.0 1.7 + - - -
884A TYR* 3.6 6.3 + - - +
885A ARG* 3.4 22.3 + - - +
1006A THR* 6.6 0.2 - - - -
1010A PHE* 3.7 25.1 - - - -
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Residues in contact with PRO 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A GLU* 4.4 7.4 - - - +
840A VAL* 3.6 22.9 - - + +
880A SER* 3.4 13.2 - - - -
881A SER* 1.3 94.6 - - - +
883A VAL* 1.3 59.5 + - + +
885A ARG* 4.4 0.2 - - - -
886A LEU* 3.6 10.9 - - - +
1006A THR* 4.6 7.4 - - + +
1009A LEU* 3.6 32.8 - - + +
1010A PHE* 3.8 13.9 - - + +
1013A SER* 2.7 31.7 + - - -
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Residues in contact with VAL 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A GLU* 4.1 16.2 - - + -
839A ILE* 3.6 39.0 - - + -
840A VAL* 4.4 4.7 - - + -
877A ALA 3.3 19.5 - - - +
878A MET* 4.5 2.9 - - - -
880A SER* 3.2 14.3 + - - +
881A SER 3.0 0.2 - - - -
882A PRO* 1.3 83.4 - - - +
884A TYR* 1.3 59.4 + - - +
885A ARG 2.8 11.6 + - - -
886A LEU* 3.0 20.6 + - + +
890A PHE* 3.2 35.1 - - + -
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Residues in contact with TYR 884 (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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878A MET 3.5 22.1 + - - +
879A ASN* 3.9 22.9 - - + +
880A SER 2.7 23.4 + - - +
881A SER* 4.4 4.3 - - - +
883A VAL* 1.3 71.6 - - - +
885A ARG* 1.3 58.3 + - + +
886A LEU 3.5 0.8 + - - -
887A ASP* 4.5 5.7 - - - +
890A PHE* 5.0 5.3 - - - -
905A HIS* 5.4 4.5 - + - -
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Residues in contact with ARG 885 (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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881A SER 3.4 16.4 + - - +
882A PRO 4.2 0.7 - - - +
883A VAL 2.8 2.2 + - - -
884A TYR* 1.3 77.8 - - + +
886A LEU* 1.3 59.8 + - - +
887A ASP* 3.0 17.7 + - - +
1010A PHE* 4.2 21.2 - - - -
1013A SER* 2.8 56.9 + - - +
1014A LEU* 3.5 19.5 - - - +
1017A GLU* 2.8 28.0 + - - +
1018A PRO 3.8 11.7 + - - -
1019A ARG* 4.5 6.3 - - - +
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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