Contacts of the strand formed by residues 999 - 1007 (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 ILE 999 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994C VAL* 4.7 6.7 - - + -
995C ALA 3.7 13.5 - - - +
996C ARG* 2.9 21.5 + - - +
997C GLU 4.0 3.5 - - - +
998C LYS* 1.3 84.5 - - + +
1000C THR* 1.3 75.7 + - - +
1001C MET* 4.6 4.9 - - + +
1017C VAL 3.3 3.1 - - - +
1018C ALA* 3.4 30.3 - - + -
1021C VAL* 5.5 1.1 - - + -
1032C ILE* 4.1 22.7 - - + -
1069C VAL* 4.1 16.8 - - + -
1076C LEU* 4.3 15.0 - - + -
1078C ILE* 3.9 18.6 - - + -
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Residues in contact with THR1000 (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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997C GLU 5.0 2.1 + - - -
998C LYS 4.6 2.6 + - - -
999C ILE* 1.3 81.9 + - - +
1001C MET* 1.3 70.4 + - - +
1002C SER* 4.1 2.3 + - - -
1016C GLY* 3.2 1.8 - - - -
1017C VAL* 3.0 43.9 + - - +
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Residues in contact with MET1001 (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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999C ILE* 4.6 3.9 - - + +
1000C THR* 1.3 77.2 - - - +
1002C SER* 1.3 69.0 + - - +
1014C TYR* 3.5 42.6 - - + -
1015C GLU 3.4 13.2 - - - +
1016C GLY* 4.0 0.7 - - - -
1032C ILE* 3.9 35.4 - - + -
1034C THR* 4.6 1.3 - - + -
1076C LEU* 4.5 16.6 - - - -
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Residues in contact with SER1002 (chain C).
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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1000C THR 4.1 4.5 + - - -
1001C MET* 1.3 80.7 + - - +
1003C ARG* 1.3 74.1 + - - +
1004C GLU 3.9 0.2 + - - -
1014C TYR* 3.8 12.1 - - - -
1015C GLU* 2.8 21.7 + - - +
1016C GLY* 4.3 4.2 - - - -
1017C VAL* 5.7 2.1 - - - +
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Residues in contact with ARG1003 (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 4.1 24.7 + - - -
1002C SER* 1.3 85.7 - - - +
1004C GLU* 1.3 66.0 + - - +
1005C LEU* 3.6 23.1 + - - +
1014C TYR* 3.5 2.5 - - - -
1015C GLU* 2.6 59.0 + - + +
1029C ARG* 5.2 3.8 - - - +
1081C LEU* 6.0 1.4 - - - +
1083C THR* 5.1 7.3 + - - +
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Residues in contact with GLU1004 (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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1002C SER 3.9 0.2 + - - -
1003C ARG* 1.3 78.7 + - - +
1005C LEU* 1.3 62.5 + - - +
1006C GLY* 4.5 3.4 - - - +
1012C MET* 3.3 35.6 - - - +
1014C TYR* 3.6 27.5 + - + -
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Residues in contact with LEU1005 (chain C).
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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1C 575 3.6 76.2 - - + -
1003C ARG* 3.6 33.3 + - - +
1004C GLU* 1.3 74.3 - - - +
1006C GLY* 1.3 55.3 + - - +
1013C VAL* 2.6 18.9 + - + +
1014C TYR 3.4 21.1 - - - +
1015C GLU* 3.7 15.0 - - + +
1031C ALA* 4.1 4.3 - - + -
1081C LEU* 3.7 20.6 - - + -
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Residues in contact with GLY1006 (chain C).
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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1C 575 4.7 4.3 - - - -
1004C GLU* 3.5 4.6 - - - -
1005C LEU* 1.3 80.0 - - - +
1007C GLN* 1.3 59.4 + - - -
1012C MET* 3.4 11.8 - - - -
1013C VAL* 2.7 40.2 + - - +
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Residues in contact with GLN1007 (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 3.6 8.8 - - - +
1006C GLY* 1.3 71.7 - - - -
1008C GLY* 1.3 70.1 + - - +
1010C PHE 5.0 0.2 - - - -
1011C GLY* 3.3 33.1 - - - +
1012C MET* 3.2 29.5 - - + +
1036C ASN* 4.4 10.1 + - - +
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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