Contacts of the strand formed by residues 1075 - 1080 (chain B) 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 THR1075 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982B SER* 5.5 0.2 + - - -
984B ALA* 4.1 23.7 - - + +
1033B LYS 3.8 0.3 - - - +
1034B THR* 3.6 4.0 - - - -
1035B VAL* 3.2 37.6 + - - +
1044B ARG* 3.7 23.8 + - - -
1047B PHE* 4.2 12.1 - - + -
1048B LEU* 4.2 20.0 - - + -
1068B VAL* 4.5 1.3 - - + -
1069B VAL 3.5 19.3 - - - +
1070B SER* 4.5 1.4 + - - +
1072B GLY 4.3 3.8 + - - -
1073B GLN* 3.9 8.4 + - - -
1074B PRO* 1.3 71.8 - - - +
1076B LEU* 1.3 62.0 + - - +
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Residues in contact with LEU1076 (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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996B ARG* 3.6 29.4 - - + +
999B ILE* 4.4 15.5 - - + -
1001B MET* 3.5 25.8 - - + -
1032B ILE* 3.9 12.8 - - + -
1033B LYS 3.4 1.3 - - - -
1034B THR* 3.4 33.2 - - + -
1068B VAL* 3.2 8.9 - - - +
1069B VAL* 2.8 55.1 + - + -
1074B PRO* 3.9 10.1 - - + +
1075B THR* 1.3 78.6 - - - +
1077B VAL* 1.3 63.9 + - - +
1078B ILE* 4.2 3.6 - - + -
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Residues in contact with VAL1077 (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 ALA 3.7 0.5 - - - +
1032B ILE* 3.6 2.6 - - - -
1033B LYS* 2.9 43.2 + - + +
1047B PHE* 3.3 35.0 - - + -
1048B LEU* 5.4 0.7 - - + -
1051B ALA* 4.0 21.3 - - + -
1065B LEU* 4.0 17.3 - - + -
1067B GLY 3.7 3.4 - - - +
1068B VAL* 4.3 12.1 - - + -
1076B LEU* 1.3 76.0 - - - +
1078B ILE* 1.3 63.3 + - - +
1079B MET* 3.8 26.8 + - + -
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Residues in contact with ILE1078 (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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994B VAL* 3.9 13.5 - - + -
999B ILE* 3.9 16.4 - - + -
1018B ALA* 4.6 6.5 - - + -
1021B VAL* 5.4 3.1 - - + -
1030B VAL* 3.6 35.2 - - + -
1031B ALA 3.6 2.2 - - - -
1032B ILE* 4.6 12.8 - - + -
1065B LEU* 3.7 3.6 - - - +
1066B LEU* 2.8 36.6 + - + -
1067B GLY* 2.8 28.6 + - - +
1069B VAL* 3.5 32.8 - - + -
1076B LEU* 4.2 6.5 - - + +
1077B VAL* 1.3 76.5 - - - +
1079B MET* 1.3 64.4 + - - +
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Residues in contact with MET1079 (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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1B 575 3.3 28.7 - - + +
1030B VAL* 3.2 10.9 - - - +
1031B ALA* 2.7 41.9 + - + +
1033B LYS* 4.2 25.1 - - + -
1054B MET* 3.7 34.8 - - + +
1063B VAL* 3.8 7.0 - - + -
1064B ARG 3.6 19.7 - - - +
1065B LEU* 3.9 14.1 - - - -
1066B LEU* 4.0 4.7 - - - -
1077B VAL* 3.8 21.8 - - + -
1078B ILE* 1.3 77.7 - - - +
1080B GLU* 1.3 59.4 + - - +
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Residues in contact with GLU1080 (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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1B 575 3.2 20.1 + - - -
1029B ARG 5.0 0.7 - - - -
1062B VAL 3.7 1.6 - - - +
1063B VAL* 3.6 11.9 - - + +
1064B ARG* 2.8 56.5 + - + +
1066B LEU* 3.9 15.4 - - + +
1079B MET* 1.3 70.2 - - - +
1081B LEU* 1.3 68.8 + - - +
1082B MET* 3.6 14.5 + - - +
1144B ALA* 5.6 1.0 - - - +
1150B LYS* 2.7 35.2 + - - -
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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