Contacts of the strand formed by residues 1012 - 1022 (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 MET1012 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004B GLU* 3.4 42.2 - - + +
1006B GLY* 3.3 25.4 - - - +
1007B GLN* 3.3 30.2 + - + +
1011B GLY* 1.3 71.9 - - - -
1013B VAL* 1.3 63.8 + - - +
1014B TYR* 3.5 37.5 - - + +
1034B THR* 3.0 30.9 + - - +
1036B ASN* 5.5 1.8 + - - -
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Residues in contact with VAL1013 (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 3.6 34.5 - - + -
1004B GLU* 3.6 5.0 - - - -
1005B LEU* 2.9 35.3 + - + -
1006B GLY 2.8 25.1 + - - +
1008B GLY 3.9 1.8 - - - +
1011B GLY 3.9 7.9 - - - +
1012B MET* 1.3 78.9 - - - +
1014B TYR* 1.3 70.4 + - - +
1031B ALA* 4.4 4.3 - - + -
1032B ILE 3.2 20.2 - - - +
1033B LYS* 3.7 28.9 - - + +
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Residues in contact with TYR1014 (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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1001B MET* 3.6 38.6 - - + -
1002B SER 5.8 0.2 - - - -
1003B ARG* 3.3 21.3 - - - +
1004B GLU* 3.6 26.3 + - + -
1005B LEU* 3.5 6.7 - - - +
1012B MET* 3.5 26.0 - - + +
1013B VAL* 1.3 74.2 - - - +
1015B GLU* 1.3 66.8 + - - +
1031B ALA* 3.4 4.9 - - - -
1032B ILE* 2.7 40.4 + - + +
1034B THR* 3.6 26.7 - - + -
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Residues in contact with GLU1015 (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 5.6 1.0 - - - -
1001B MET* 3.4 5.2 - - - -
1002B SER* 2.6 42.3 + - - -
1003B ARG* 2.6 54.8 + - + +
1005B LEU* 3.7 17.6 - - + +
1014B TYR* 1.3 77.5 - - - +
1016B GLY* 1.3 59.2 + - - +
1029B ARG* 2.7 33.7 + - - -
1030B VAL 3.7 2.7 - - - -
1032B ILE* 4.2 2.0 - - - -
1081B LEU* 3.7 22.9 - - + -
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Residues in contact with GLY1016 (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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1000B THR 3.0 13.0 - - - -
1002B SER* 3.9 10.8 - - - -
1015B GLU* 1.3 83.1 - - - +
1017B VAL* 1.3 61.9 + - - +
1029B ARG* 3.4 6.8 + - - +
1030B VAL* 2.7 41.3 + - - -
1032B ILE* 4.0 4.7 - - - +
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Residues in contact with VAL1017 (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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998B LYS 3.7 1.0 - - - +
999B ILE* 3.6 6.1 - - - +
1000B THR* 3.0 40.2 + - - +
1002B SER* 5.0 6.3 - - - +
1016B GLY* 1.3 79.1 - - - +
1018B ALA* 1.3 65.1 + - - +
1027B GLU* 3.7 44.9 - - + +
1028B THR 3.2 15.3 - - - +
1029B ARG* 5.1 7.9 - - + -
1030B VAL* 4.1 2.0 - - - -
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Residues in contact with ALA1018 (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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998B LYS 3.3 4.7 - - - -
999B ILE* 3.7 20.6 - - + -
1017B VAL* 1.3 78.9 - - - +
1019B LYS* 1.3 63.8 + - - +
1020B GLY 3.4 2.6 + - - -
1021B VAL* 3.8 30.7 - - + +
1026B PRO 3.7 0.2 - - - +
1028B THR* 2.8 28.7 + - - -
1030B VAL* 4.0 17.5 - - + -
1078B ILE* 4.6 2.0 - - + -
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Residues in contact with LYS1019 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1267A LYS* 5.6 10.3 - - - +
1268A GLU* 5.0 8.3 - - - +
1275A ARG* 6.1 1.8 - - - +
997B GLU 4.9 9.1 + - - +
998B LYS* 2.7 54.1 + - + +
1000B THR* 5.3 6.5 + - - -
1017B VAL* 6.0 0.2 - - + -
1018B ALA* 1.3 68.6 - - - +
1020B GLY* 1.3 64.5 + - - +
1021B VAL* 4.0 2.1 - - - +
1026B PRO 3.3 6.1 - - - +
1027B GLU* 4.0 31.3 + - + +
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Residues in contact with GLY1020 (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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1268A GLU* 4.1 28.0 - - - +
998B LYS* 4.6 5.0 - - - +
1018B ALA 3.4 1.2 + - - -
1019B LYS* 1.3 74.5 - - - +
1021B VAL* 1.3 61.8 + - - +
1022B VAL 3.6 2.7 - - - -
1025B GLU 3.9 9.9 - - - -
1026B PRO* 2.7 18.3 + - - -
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Residues in contact with VAL1021 (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* 4.2 30.7 - - + -
998B LYS* 5.3 0.9 - - + -
999B ILE* 5.1 0.7 - - + -
1018B ALA* 3.8 39.5 - - + +
1019B LYS 4.0 6.1 - - - +
1020B GLY* 1.3 78.7 - - - +
1022B VAL* 1.3 75.0 + - + +
1025B GLU 4.6 0.6 + - - -
1028B THR* 4.0 11.2 + - - -
1066B LEU* 4.5 34.5 - - + +
1078B ILE* 5.4 3.4 - - + -
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Residues in contact with VAL1022 (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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1020B GLY* 3.6 2.0 - - - -
1021B VAL* 1.3 93.8 + - + +
1023B LYS* 1.3 75.9 + - + +
1024B ASP 3.4 0.3 + - - -
1025B GLU* 3.1 48.7 + - + +
1028B THR* 3.9 15.9 + - + +
1066B LEU* 4.1 23.6 - - + -
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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