Contacts of the strand formed by residues 1042 - 1047 (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 ALA1042 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036B VAL* 3.4 23.2 + - + -
1039B ASP* 3.2 25.8 + - + +
1041B ARG* 1.3 82.4 - - - +
1043B PHE* 1.3 62.2 + - - +
1058B GLU* 4.4 10.3 - - + +
1059B LEU 3.2 11.4 - - - +
1060B VAL* 4.2 11.2 - - + -
1067B LYS* 3.2 23.4 + - - -
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Residues in contact with PHE1043 (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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972B LEU* 3.8 26.5 - - + -
1033B ILE* 5.3 0.9 - - + -
1034B ARG 3.5 10.5 - - - +
1035B SER* 4.2 1.8 - - - -
1036B VAL* 3.8 9.2 - - - +
1041B ARG 4.7 0.7 - - - -
1042B ALA* 1.3 80.0 - - - +
1044B PHE* 1.3 61.8 + - - +
1045B ILE* 3.7 24.4 + - + -
1058B GLU* 3.7 2.3 - - - -
1059B LEU* 3.0 46.1 + - + +
1061B ALA* 4.8 11.4 - - + -
1067B LYS* 4.0 18.2 - - + -
1070B TRP* 3.9 28.5 - + + -
1071B MET* 3.8 21.5 - - + -
1074B LEU* 3.6 23.3 - - + -
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Residues in contact with PHE1044 (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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1032B LEU 3.5 1.1 - - - +
1033B ILE* 3.7 1.0 - - - -
1034B ARG* 2.5 46.4 + - + +
1035B SER 4.5 1.3 - - - -
1036B VAL* 3.6 29.8 - - + -
1043B PHE* 1.3 74.6 - - - +
1045B ILE* 1.3 67.5 + - - +
1046B ILE* 4.0 12.1 - - + -
1056B ILE* 3.6 27.1 - - + -
1057B TYR 3.5 0.7 - - - -
1058B GLU* 3.5 39.3 - - + -
39E PHE* 4.3 14.8 - + - -
41E ASN* 3.7 22.2 - - - -
58E TRP* 3.7 34.1 - + - -
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Residues in contact with ILE1045 (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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993B LEU* 3.5 28.3 - - + -
1026B LEU* 3.8 25.1 - - + -
1031B VAL* 4.1 20.0 - - + -
1032B LEU 3.5 2.5 - - - -
1033B ILE* 3.8 16.4 - - + -
1043B PHE* 3.7 28.9 + - + -
1044B PHE* 1.3 79.7 - - - +
1046B ILE* 1.3 60.5 + - - +
1057B TYR* 2.9 48.0 + - + +
1059B LEU* 3.8 10.5 - - + -
1074B LEU* 3.8 11.2 - - + -
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Residues in contact with ILE1046 (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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1031B VAL* 3.2 6.1 - - - -
1032B LEU* 2.9 54.4 + - + +
1034B ARG* 5.2 2.5 - - + -
1044B PHE* 4.6 9.4 - - + -
1045B ILE* 1.3 71.7 - - - +
1047B CYS* 1.3 68.2 + - - +
1048B THR* 3.5 10.8 + - + +
1055B GLN 3.3 11.7 - - - +
1056B ILE* 4.0 13.0 - - + +
39E PHE* 3.6 52.3 - - + -
69E LEU* 4.7 5.4 - - + -
72E LEU* 3.7 23.1 - - + -
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Residues in contact with CYS1047 (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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952B LEU* 5.1 12.8 - - - -
1023B SER* 6.2 0.4 - - - -
1026B LEU* 3.6 33.7 - - + -
1027B LYS 6.1 0.7 - - - -
1030B ALA 3.7 7.6 - - - -
1031B VAL* 3.9 5.1 - - + +
1045B ILE 3.5 2.4 + - - -
1046B ILE* 1.3 72.1 - - - +
1048B THR* 1.3 58.4 + - - +
1049B SER* 3.6 28.3 - - - -
1053B PRO 5.6 2.0 - - - -
1054B PRO* 3.5 10.0 - - - +
1055B GLN* 2.8 36.3 + - + +
1057B TYR* 4.0 8.5 - - + -
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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