Contacts of the strand formed by residues 103 - 106 (chain C) in PDB entry 2Q5E
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 CYS 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C LEU* 4.0 7.0 - - - -
101C ARG 3.6 2.4 + - - -
102C ILE* 1.3 73.6 - - - +
104C VAL* 1.3 61.1 + - - +
105C VAL* 4.2 6.7 - - - -
158C GLU* 3.2 23.1 - - - +
160C VAL* 3.8 27.8 - - - -
206C LEU* 4.1 10.5 - - - -
208C ARG* 3.6 33.4 - - + -
212C LYS 3.1 8.8 + - - +
213C THR* 3.2 7.3 - - - +
214C LEU 3.0 22.0 + - - -
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Residues in contact with VAL 104 (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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102C ILE* 4.2 3.6 - - + -
103C CYS* 1.3 75.5 - - - +
105C VAL* 1.3 66.6 + - - +
106C ILE* 3.9 21.4 + - + +
153C MET* 4.2 16.2 - - + -
157C PHE* 3.4 45.5 - - + -
158C GLU 2.8 9.4 + - - +
159C CYS* 3.5 3.5 - - - -
160C VAL* 2.8 26.3 + - - +
214C LEU* 3.4 14.8 - - + +
216C LEU* 4.6 5.4 - - + -
252C PHE* 4.4 18.2 - - + -
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Residues in contact with VAL 105 (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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103C CYS* 4.2 3.6 - - - -
104C VAL* 1.3 74.7 - - - +
106C ILE* 1.3 59.8 + - - +
160C VAL* 3.5 23.6 - - + -
162C PHE* 3.8 26.2 - - + -
201C LYS* 5.4 0.4 - - + -
203C LEU* 4.4 7.4 - - + -
206C LEU* 3.9 38.4 - - + -
213C THR* 5.1 0.7 - - + -
214C LEU 3.0 10.5 + - - +
215C ILE* 4.0 26.1 - - + +
216C LEU* 2.9 27.4 + - - +
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Residues in contact with ILE 106 (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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104C VAL* 3.9 22.9 - - + +
105C VAL* 1.3 79.2 - - - +
107C ASP* 1.3 67.2 + - - +
111C THR* 4.8 0.4 - - + -
112C LEU* 3.5 35.7 - - + -
149C PHE* 4.6 7.0 - - + -
150C LEU* 4.5 14.4 - - + -
153C MET* 4.6 9.6 - - + -
159C CYS* 4.7 12.1 - - + -
160C VAL 2.8 13.4 + - - +
161C LEU* 3.5 8.1 - - - +
162C PHE 2.8 27.3 + - - +
183C PHE* 4.3 18.8 - - + -
216C LEU* 3.6 24.0 - - + +
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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