Contacts of the strand formed by residues 930 - 934 (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 ARG 930 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557C VAL 3.0 23.2 + - - -
558C PHE* 2.8 26.3 + - - +
560C ARG* 3.3 31.5 + - - +
927C ILE 4.7 0.8 + - - -
928C TRP* 2.8 35.5 + - - +
929C ASP* 1.3 75.4 - - - +
931C PHE* 1.3 68.1 + - - +
932C ASP* 3.5 24.7 + - - +
1018C PRO* 4.0 4.3 - - - -
1019C PHE* 3.3 51.0 - - + +
1021C THR* 3.6 21.9 + - - +
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Residues in contact with PHE 931 (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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919C TYR* 3.4 20.9 - + - -
930C ARG* 1.3 73.5 - - - +
932C ASP* 1.3 60.3 + - - +
933C ILE* 4.7 4.5 - - + -
945C HIS* 5.7 5.2 - - - +
946C PHE* 3.4 39.5 - + + -
950C GLU* 3.4 38.1 - - + -
952C LEU* 4.0 4.7 - - + -
1005C ILE* 5.3 0.2 - - + -
1017C VAL* 4.2 7.0 - - + -
1018C PRO* 3.6 41.7 - - + -
1019C PHE 2.9 18.3 + - - +
1020C ILE* 3.5 9.1 - - + +
1021C THR* 3.0 27.0 + - - +
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Residues in contact with ASP 932 (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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560C ARG* 3.6 32.0 + - - -
930C ARG* 3.5 16.2 + - - +
931C PHE* 1.3 73.5 - - - +
933C ILE* 1.3 65.2 + - - +
934C LYS 4.3 0.3 + - - -
945C HIS* 5.3 4.3 + - - -
1021C THR* 3.9 9.2 - - - +
1023C HIS* 2.8 30.1 + - + +
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Residues in contact with ILE 933 (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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931C PHE* 4.5 3.8 - - + +
932C ASP* 1.3 80.0 - - - +
934C LYS* 1.3 73.0 + - - +
935C GLY 3.8 7.5 - - - +
937C ILE* 4.3 23.1 - - + -
942C LEU* 4.2 15.9 - - + -
945C HIS* 4.6 16.4 - - + +
946C PHE* 4.1 21.8 - - + -
1020C ILE* 3.7 27.1 - - + -
1021C THR 3.2 12.0 + - - +
1022C ILE* 4.2 8.3 - - + -
1023C HIS* 3.0 34.1 + - - +
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Residues in contact with LYS 934 (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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932C ASP 4.3 1.0 + - - -
933C ILE* 1.3 75.6 - - - +
935C GLY* 1.3 69.3 + - - +
937C ILE* 3.8 15.2 - - - +
1023C HIS* 4.4 3.6 - - - -
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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