Contacts of the strand formed by residues 992 - 998 (chain B) in PDB entry 3KZ1
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 LEU 992 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956B PHE* 3.7 35.9 - - + -
959B LEU* 3.8 14.8 - - + -
964B ARG* 3.7 31.0 - - - +
988B LEU* 4.1 0.5 - - - +
989B LEU* 2.8 45.1 + - + +
991B ASP* 1.3 106.0 + - + +
993B LEU* 1.3 59.2 + - - +
994B VAL* 4.1 1.6 - - + -
1025B VAL* 4.0 12.6 - - + -
1026B LEU 3.5 3.8 - - - +
1027B LYS* 3.9 17.0 - - + -
1028B LEU* 3.6 7.9 - - - +
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Residues in contact with LEU 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986B VAL* 3.8 23.1 - - + -
987B LEU 3.6 6.5 - - - +
988B LEU* 4.0 24.0 - - + -
992B LEU* 1.3 73.7 - - - +
994B VAL* 1.3 63.1 + - - +
995B LEU* 4.0 18.9 + - + +
1024B PRO 3.9 1.2 - - - +
1025B VAL* 3.5 1.9 - - - +
1026B LEU* 2.8 55.8 + - + +
1028B LEU* 4.3 12.3 - - + +
1031B VAL* 6.5 0.4 - - + -
1045B ILE* 3.5 32.3 - - + -
1059B LEU* 4.7 2.0 - - + -
1070B TRP* 4.7 2.2 - - + -
1074B LEU* 4.1 13.9 - - + -
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Residues in contact with VAL 994 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959B LEU* 4.6 9.4 - - + -
961B LEU* 4.3 8.3 - - + -
985B HIS 4.0 0.3 - - - +
986B VAL* 3.4 4.7 - - - +
987B LEU* 3.0 55.2 + - + +
989B LEU* 3.9 22.4 - - + -
992B LEU* 5.1 2.2 - - + -
993B LEU* 1.3 74.3 - - - +
995B LEU* 1.3 64.2 + - - +
996B LEU* 3.7 28.1 + - + -
1005B LEU* 3.9 19.7 - - + -
1024B PRO 3.6 3.1 - - - +
1025B VAL* 4.5 10.8 - - + +
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Residues in contact with LEU 995 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974B TRP* 4.8 8.3 - - + -
984B LEU* 3.7 29.7 - - + +
985B HIS 4.4 1.3 - - - -
986B VAL* 3.9 22.4 - - + -
993B LEU* 4.0 20.9 - - + +
994B VAL* 1.3 75.8 - - - +
996B LEU* 1.3 61.8 + - - +
1004B LEU 4.2 4.5 - - - +
1005B LEU* 4.3 2.8 - - - +
1008B HIS* 5.4 3.4 + - - +
1023B SER 4.2 4.3 - - - +
1024B PRO* 2.7 41.6 + - + +
1026B LEU* 5.0 6.3 - - + -
1057B TYR* 3.7 37.0 - - + -
1059B LEU* 4.4 12.6 - - + -
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Residues in contact with LEU 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936B TYR* 5.7 1.1 - - + -
940B LEU* 3.8 22.2 - - + -
961B LEU* 5.6 3.4 - - + -
984B LEU* 2.9 19.3 - - - +
985B HIS* 3.0 38.8 + - + +
987B LEU* 3.9 36.8 - - + -
994B VAL* 3.8 17.7 - - + -
995B LEU* 1.3 72.7 - - - +
997B GLN* 1.3 58.5 + - - +
998B LYS 4.2 0.2 - - - -
1003B LEU* 3.7 47.6 - - + -
1004B LEU 3.8 13.5 - - - +
1005B LEU* 4.3 3.4 - - + -
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Residues in contact with GLN 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982B LEU* 3.2 36.8 - - + +
983B ASP 4.5 10.7 - - - +
984B LEU* 4.4 6.7 - - + -
996B LEU* 1.3 74.1 - - - +
998B LYS* 1.3 73.5 + - - +
999B GLN* 3.8 0.6 + - + -
1003B LEU* 3.6 2.6 - - - -
1004B LEU* 2.8 56.4 + - + +
1006B LYS* 3.8 28.5 - - + +
1008B HIS* 3.9 12.3 - - + +
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Residues in contact with LYS 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939B ARG* 4.1 18.8 - - - +
983B ASP 5.0 3.0 + - - -
985B HIS* 5.0 19.4 - - + +
996B LEU 4.2 0.8 + - - -
997B GLN* 1.3 83.9 - - - +
999B GLN* 1.3 63.9 + - - +
1000B ASP 4.8 9.9 - - - +
1002B LYS 3.4 6.7 - - - +
1003B LEU* 3.8 20.6 - - + -
1004B LEU* 5.4 0.2 - - - -
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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