Contacts of the strand formed by residues 4188 - 4193 (chain A) in PDB entry 3CMT
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 LEU4188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4040A ILE* 4.9 13.9 - - + -
4056A LEU* 4.0 19.1 - - + -
4057A PRO 3.3 24.5 - - - +
4058A MET* 4.1 11.9 - - - -
4059A GLY 3.6 3.2 - - - +
4060A ARG 3.5 9.9 - - - +
4062A VAL* 3.8 24.5 - - + -
4079A VAL* 5.0 3.1 - - + -
4139A ASP 2.9 12.3 + - - +
4140A VAL* 3.3 13.7 - - + -
4141A ILE 2.8 26.5 + - - +
4186A ASN 3.9 1.2 + - - -
4187A THR* 1.3 75.7 - - - +
4189A LEU* 1.3 67.4 + - - +
4190A ILE* 3.9 29.4 - - + -
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Residues in contact with LEU4189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4060A ARG 3.0 9.7 + - - +
4061A ILE* 3.4 5.6 - - + +
4062A VAL* 2.9 27.4 + - - +
4129A CYS* 4.7 8.1 - - + -
4141A ILE* 3.2 20.6 - - + +
4143A VAL* 3.9 17.7 - - + -
4178A LEU* 3.8 17.0 - - + -
4182A LEU* 3.7 39.0 - - + -
4187A THR 3.8 0.2 + - - -
4188A LEU* 1.3 74.7 - - - +
4190A ILE* 1.3 75.1 + - - +
4191A PHE* 3.5 35.2 + - + -
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Residues in contact with ILE4190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4056A LEU* 3.8 22.9 - - + -
4062A VAL* 3.4 19.3 - - + +
4064A ILE* 3.6 29.8 - - + -
4076A THR* 4.0 12.6 - - - +
4079A VAL* 3.9 26.0 - - + -
4140A VAL* 4.7 6.3 - - + -
4141A ILE 2.8 10.1 + - - +
4142A VAL* 3.2 14.4 - - + +
4143A VAL 2.8 28.4 + - - +
4188A LEU* 3.9 18.2 - - + -
4189A LEU* 1.3 78.9 - - - +
4191A PHE* 1.3 66.6 + - - +
4192A ILE* 4.7 0.9 - - + +
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Residues in contact with PHE4191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4061A ILE* 3.7 26.0 - - + -
4062A VAL 2.7 12.6 + - - +
4063A GLU* 3.3 3.3 - - - +
4064A ILE 2.9 26.3 + - - -
4126A LEU* 4.2 21.3 - - + -
4129A CYS* 5.6 0.2 - - - -
4143A VAL* 3.7 31.2 - - + -
4146A VAL* 3.8 19.5 - - + -
4149A LEU* 4.5 4.0 - - + -
4171A MET* 4.8 3.6 - - + -
4175A MET* 3.8 27.6 - - + -
4178A LEU* 4.4 1.8 - - + -
4189A LEU* 3.5 33.9 - - + -
4190A ILE* 1.3 71.8 - - - +
4192A ILE* 1.3 63.3 + - - +
4215A LEU* 3.7 25.8 - - + -
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Residues in contact with ILE4192 (chain A).
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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4064A ILE* 3.4 7.9 - - + +
4072A LYS* 3.6 54.1 - - + +
4073A THR* 3.9 2.5 - - - -
4076A THR* 3.4 33.0 - - + +
4142A VAL* 4.4 3.6 - - + -
4143A VAL 2.9 11.0 + - - +
4144A ASP* 3.4 36.6 - - + +
4145A SER* 3.0 16.6 - - - +
4146A VAL* 2.8 27.8 + - - +
4190A ILE* 4.8 3.1 - - + -
4191A PHE* 1.3 74.8 - - - +
4193A ASN* 1.3 63.1 + - - +
4501A ALF 5.5 0.2 - - - -
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Residues in contact with ASN4193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4063A GLU* 3.1 20.7 - - + +
4064A ILE 2.8 8.0 + - - +
4065A TYR* 3.3 28.9 - - + -
4066A GLY 3.7 0.3 + - - -
4072A LYS* 3.4 12.8 - - - +
4145A SER* 4.9 0.2 - - - +
4146A VAL* 3.3 20.4 - - + +
4147A ALA 3.9 2.4 - - - +
4191A PHE 3.8 0.2 + - - -
4192A ILE* 1.3 75.6 - - - +
4194A GLN* 1.3 80.8 + - - +
4209A THR* 3.0 14.1 - - - +
4210A THR* 2.9 53.8 + - - +
4215A LEU* 4.5 1.4 - - - +
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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