Contacts of the strand formed by residues 953 - 959 (chain C) in PDB entry 3CMM
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 GLU 953 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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943C ILE* 5.8 3.4 - - + -
947C GLU* 4.2 11.0 + - - +
951C GLY 4.1 1.0 + - - -
952C LEU* 1.3 71.6 - - - +
954C ILE* 1.3 67.9 + - - +
1007C ALA* 3.2 3.4 - - - -
1008C ASP* 2.8 57.2 + - + +
1009C ASP 4.8 6.5 - - - +
1012C GLY* 5.6 2.8 - - - -
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Residues in contact with ILE 954 (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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942C LEU* 3.6 29.4 - - + -
943C ILE* 4.1 23.8 - - + +
946C PHE* 3.6 32.5 - - + -
952C LEU* 3.9 1.3 + - + +
953C GLU* 1.3 79.8 - - - +
955C THR* 1.3 62.0 + - - +
956C MET 3.5 25.4 - - - +
957C LEU* 4.6 1.8 - - + -
965C TYR* 3.5 34.5 + - + -
967C SER* 4.3 3.3 + - - -
1005C ILE* 3.6 22.7 - - + -
1006C CYS 3.3 3.6 - - - +
1007C ALA* 4.3 4.5 - - + +
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Residues in contact with THR 955 (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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953C GLU 3.5 0.2 + - - -
954C ILE* 1.3 73.7 - - - +
956C MET* 1.3 66.6 + - + +
965C TYR* 4.5 0.7 - - - -
966C ALA* 3.0 5.9 - - - -
967C SER* 2.9 49.2 + - - +
968C PHE* 6.3 1.8 - - + -
1006C CYS* 2.7 21.2 + - + +
1007C ALA* 3.5 23.9 + - - -
1008C ASP* 3.7 14.4 + - - +
1014C ASP* 4.6 6.5 + - - +
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Residues in contact with MET 956 (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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954C ILE* 3.6 3.6 - - - -
955C THR* 1.3 92.4 - - + +
957C LEU* 1.3 61.2 + - - +
958C SER* 6.0 0.7 - - - +
963C LEU* 3.3 37.9 - - + -
965C TYR 3.4 6.3 - - - +
966C ALA* 3.9 9.6 - - + -
968C PHE* 4.0 18.6 - - + -
1004C GLU 4.5 0.2 - - - -
1005C ILE* 3.1 11.3 - - - +
1006C CYS* 2.8 46.1 + - + +
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Residues in contact with LEU 957 (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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939C LEU* 4.5 11.9 - - + -
942C LEU* 3.5 41.1 - - + -
954C ILE* 5.2 1.6 - - + -
956C MET* 1.3 77.2 - - - +
958C SER* 1.3 57.9 + - - +
963C LEU* 3.8 1.5 - - - +
964C LEU* 2.7 66.3 + - + +
965C TYR* 3.0 24.5 + - + +
982C ILE* 5.6 2.2 - - + -
985C LEU* 4.9 5.2 - - + -
1003C LEU* 3.7 20.9 - - + -
1004C GLU 3.4 6.5 - - - +
1005C ILE* 3.6 14.4 - - + -
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Residues in contact with SER 958 (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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956C MET* 5.8 0.9 - - - +
957C LEU* 1.3 75.5 - - - +
959C TYR* 1.3 59.3 + - - +
960C GLY 3.9 12.1 + - - -
961C VAL 5.1 1.1 - - - -
962C SER 3.2 20.0 - - - -
963C LEU* 4.1 9.2 - - - -
964C LEU* 4.2 4.0 - - - +
1003C LEU* 3.3 9.9 - - - +
1004C GLU* 2.8 49.1 + - - +
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Residues in contact with TYR 959 (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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958C SER* 1.3 72.5 - - - +
960C GLY* 1.3 66.8 + - - +
961C VAL 3.3 0.5 + - - -
962C SER* 3.0 27.9 + - - +
964C LEU* 3.9 17.1 - - + +
986C VAL* 3.6 33.4 - - + -
990C THR* 5.1 4.7 - - + -
993C ASP* 5.1 8.0 + - - -
995C PRO* 5.7 4.2 - - - +
998C VAL* 5.4 5.9 - - - +
1000C THR 5.0 1.9 + - - -
1001C MET* 3.5 38.2 - - + +
1002C ILE* 3.3 22.4 - - + -
1003C LEU* 3.8 17.3 - - + -
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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