Contacts of the strand formed by residues 3090 - 3093 (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 CYS3090 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3080A ILE* 3.8 37.7 - - + -
3083A ALA* 3.9 14.6 - - - -
3084A GLN* 4.0 14.1 - - - +
3088A LYS 3.9 2.9 + - - -
3089A THR* 1.3 79.4 - - - +
3091A ALA* 1.3 60.3 + - - +
3113A ASN 4.1 4.0 + - - +
3114A LEU* 3.3 9.3 - - + +
3115A LEU* 3.0 27.7 + - - +
3138A VAL* 4.1 2.2 - - - -
3140A VAL* 3.1 34.3 - - - +
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Residues in contact with ALA3091 (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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3080A ILE* 4.7 0.7 - - - +
3090A CYS* 1.3 76.1 - - - +
3092A PHE* 1.3 60.1 + - - +
3093A ILE* 4.2 3.6 - - + -
3114A LEU* 4.2 2.0 - - - -
3115A LEU* 3.2 17.7 - - + +
3132A LEU* 3.7 30.7 - - + -
3138A VAL* 3.9 10.3 - - + +
3140A VAL 2.9 7.4 + - - +
3141A ILE* 3.4 9.5 - - + -
3142A VAL* 3.0 29.0 + - - +
4026A ILE* 5.3 0.9 - - + -
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Residues in contact with PHE3092 (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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3073A THR* 4.1 9.2 - - + -
3076A THR* 3.5 25.4 - - + -
3077A LEU* 4.0 14.1 - - + -
3080A ILE* 3.9 15.7 - - + -
3091A ALA* 1.3 74.0 - - - +
3093A ILE* 1.3 64.6 + - - +
3094A ASP* 3.6 34.1 + - + -
3099A LEU* 3.6 26.5 - - + -
3114A LEU* 3.8 22.9 - - + -
3115A LEU 2.7 8.3 + - - +
3116A CYS* 3.3 3.7 - - - -
3117A SER 3.0 24.4 + - - -
3142A VAL* 3.6 15.5 - - + -
3144A ASP* 3.5 30.5 - - + -
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Residues in contact with ILE3093 (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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3091A ALA* 4.9 1.1 - - + -
3092A PHE* 1.3 79.2 - - - +
3094A ASP* 1.3 58.3 + - - +
3095A ALA* 3.1 5.7 + - + +
3117A SER* 3.6 12.3 - - - +
3119A PRO* 3.8 30.1 - - + -
3125A ALA* 4.0 17.9 - - + +
3128A ILE* 3.9 27.1 - - + -
3129A CYS* 4.1 13.9 - - - -
3132A LEU* 4.7 7.0 - - + -
3141A ILE* 4.0 21.8 - - + -
3142A VAL 2.7 18.4 + - - +
3143A VAL* 3.6 12.5 - - + +
3144A ASP 2.9 28.1 + - - -
4026A ILE* 5.5 0.9 - - + -
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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