Contacts of the strand formed by residues 1076 - 1080 (chain C) in PDB entry 2ZM3
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 LEU1076 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996C ARG* 3.9 20.4 - - + +
999C ILE* 4.3 18.6 - - + -
1001C MET* 4.5 10.5 - - - -
1032C ILE* 3.6 20.6 - - + -
1033C LYS 3.4 1.1 - - - -
1034C THR* 3.5 31.9 - - + -
1068C VAL* 3.1 12.1 - - - +
1069C VAL* 2.9 56.8 + - + -
1074C PRO* 3.7 15.3 - - + +
1075C THR* 1.3 78.3 - - - +
1077C VAL* 1.3 63.5 + - - +
1078C ILE* 4.2 3.4 - - + -
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Residues in contact with VAL1077 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C ALA 3.7 0.5 - - - +
1032C ILE* 3.8 0.6 - - - -
1033C LYS* 2.9 44.1 + - + +
1047C PHE* 3.4 36.6 - - + -
1048C LEU* 5.3 1.8 - - + -
1051C ALA* 4.2 17.5 - - + -
1065C LEU* 3.6 29.4 - - + -
1067C GLY 3.8 4.0 - - - +
1068C VAL* 4.2 13.5 - - + -
1076C LEU* 1.3 77.9 - - - +
1078C ILE* 1.3 62.1 + - - +
1079C MET* 3.7 14.2 + - - +
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Residues in contact with ILE1078 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994C VAL* 3.6 29.4 - - + -
999C ILE* 3.9 15.0 - - + -
1018C ALA* 4.7 4.9 - - + -
1021C VAL* 4.9 3.1 - - + -
1030C VAL* 3.6 26.9 - - + -
1031C ALA 3.7 2.2 - - - -
1032C ILE* 3.6 21.1 - - + -
1065C LEU* 3.7 4.5 - - - +
1066C LEU* 2.7 50.7 + - + -
1067C GLY* 2.8 21.0 + - - +
1069C VAL* 3.7 20.0 - - + +
1076C LEU* 4.3 6.7 - - + -
1077C VAL* 1.3 74.5 - - - +
1079C MET* 1.3 57.6 + - - +
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Residues in contact with MET1079 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C 575 3.5 28.5 - - + +
1030C VAL* 3.4 10.2 - - - +
1031C ALA* 2.8 34.3 + - + +
1033C LYS* 3.6 34.1 - - + +
1054C MET* 4.0 25.4 - - + +
1063C VAL* 3.9 11.4 - - + +
1064C ARG 3.4 22.0 - - - +
1065C LEU* 3.7 32.8 - - - +
1066C LEU* 3.6 5.6 - - - +
1077C VAL* 4.0 6.7 - - - +
1078C ILE* 1.3 75.0 - - - +
1080C GLU* 1.3 61.2 + - - +
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Residues in contact with GLU1080 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C 575 3.2 22.5 + - - -
1029C ARG 5.1 0.7 - - - -
1031C ALA* 4.2 0.2 - - - +
1062C VAL 3.8 3.8 - - - +
1063C VAL* 3.7 10.2 - - + +
1064C ARG* 2.8 55.1 + - + +
1066C LEU* 3.9 13.1 - - + +
1079C MET* 1.3 71.3 - - - +
1081C LEU* 1.3 67.7 + - - +
1082C MET* 3.7 9.2 + - - +
1144C ALA* 5.6 0.3 - - - +
1150C LYS* 3.0 37.2 + - - +
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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