Contacts of the strand formed by residues 999 - 1007 (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 ILE 999 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994B VAL* 3.8 24.2 - - + -
995B ALA 3.8 9.4 - - - +
996B ARG* 2.9 24.4 + - + +
997B GLU 3.9 4.9 - - - +
998B LYS* 1.3 81.5 - - + +
1000B THR* 1.3 71.3 + - - +
1001B MET* 4.8 3.4 - - + -
1017B VAL 3.6 3.6 - - - +
1018B ALA* 3.7 25.8 - - + -
1032B ILE* 3.9 26.2 - - + -
1069B VAL* 4.5 6.3 - - + -
1076B LEU* 4.4 17.7 - - + -
1078B ILE* 3.9 15.0 - - + -
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Residues in contact with THR1000 (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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997B GLU 5.1 1.7 + - - -
998B LYS 4.7 2.6 + - - -
999B ILE* 1.3 78.8 + - - +
1001B MET* 1.3 69.1 + - - +
1002B SER* 4.8 1.0 + - - -
1016B GLY* 3.0 5.7 - - - -
1017B VAL* 3.0 45.4 + - - +
1019B LYS* 5.3 6.8 + - - -
1032B ILE* 4.1 1.4 - - - +
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Residues in contact with MET1001 (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* 5.5 0.4 - - - +
999B ILE* 4.8 3.6 - - + -
1000B THR* 1.3 79.5 - - - +
1002B SER* 1.3 63.4 + - - +
1014B TYR* 3.6 40.2 - - + -
1015B GLU 3.4 6.3 - - - +
1016B GLY* 4.3 0.2 - - - -
1032B ILE* 3.7 21.5 - - + -
1034B THR* 4.0 4.7 - - + -
1074B PRO* 5.4 5.8 - - + -
1076B LEU* 3.5 45.1 - - + -
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Residues in contact with SER1002 (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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1000B THR 3.9 1.5 + - - -
1001B MET* 1.3 74.3 - - - +
1003B ARG* 1.3 66.6 + - - +
1014B TYR* 5.8 0.2 - - - -
1015B GLU* 2.6 32.3 + - - +
1016B GLY* 3.9 10.8 - - - -
1017B VAL* 5.0 6.2 - - - +
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Residues in contact with ARG1003 (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 5.3 9.3 - - - -
1001B MET 4.0 0.4 - - - -
1002B SER* 1.3 85.1 - - - +
1004B GLU* 1.3 68.8 + - - +
1005B LEU* 4.4 10.3 - - - +
1014B TYR* 3.3 10.5 - - - -
1015B GLU* 2.6 68.2 + - + +
1029B ARG* 5.7 1.2 - - - +
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Residues in contact with GLU1004 (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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1003B ARG* 1.3 92.0 + - - +
1005B LEU* 1.3 62.6 + - - +
1012B MET* 3.4 37.9 - - - +
1013B VAL 3.6 5.2 - - - -
1014B TYR* 3.6 25.8 + - + -
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Residues in contact with LEU1005 (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 3.7 78.3 - - + +
1003B ARG* 4.4 4.3 - - - +
1004B GLU* 1.3 78.3 - - - +
1006B GLY* 1.3 59.2 + - - +
1013B VAL* 2.9 18.5 + - + +
1014B TYR 3.5 22.7 - - - +
1015B GLU* 3.7 37.2 - - + +
1031B ALA* 4.1 1.6 - - + -
1081B LEU* 4.0 10.1 - - + -
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Residues in contact with GLY1006 (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 4.6 6.7 - - - +
1004B GLU* 5.5 0.2 - - - -
1005B LEU* 1.3 82.2 - - - +
1007B GLN* 1.3 59.9 + - - -
1012B MET* 3.3 10.5 - - - +
1013B VAL* 2.8 34.2 + - - +
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Residues in contact with GLN1007 (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 3.7 9.3 - - - +
1006B GLY* 1.3 72.4 - - - -
1008B GLY* 1.3 69.0 + - - +
1009B SER 5.4 0.2 - - - -
1010B PHE 4.6 0.6 - - - -
1011B GLY* 3.1 32.3 + - - +
1012B MET* 3.3 31.0 + - + +
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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