Contacts of the strand formed by residues 90 - 94 (chain B) in PDB entry 6CIM
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 GLN 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 4.0 2.2 - - - -
79B SER* 3.7 1.7 - - - -
80B TYR* 2.9 72.0 + - + +
81B LYS 5.6 2.0 - - - -
89B HIS* 1.3 82.8 - - - +
91B TYR* 1.3 65.8 + - - +
92B ILE* 5.8 0.2 - - + -
109B ILE* 3.9 29.6 - - + +
110B MET 3.2 15.0 - - - +
111B SER* 4.1 12.7 - - - -
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 4.5 5.7 + - - -
22B MET* 3.6 40.4 - - + -
23B ASN* 3.3 45.9 + - - +
24B PHE* 3.5 22.0 - + - -
77B THR* 5.0 11.0 - - - -
78B CYS* 3.7 19.3 - - - -
79B SER* 3.9 13.9 + - - -
89B HIS* 3.7 12.2 + - - -
90B GLN* 1.3 77.6 - - - +
92B ILE* 1.3 62.8 + - - +
93B ILE* 4.0 1.2 + - + +
108B TYR 3.6 1.2 - - - +
109B ILE* 3.2 6.3 - - - -
110B MET* 2.8 44.6 + - + +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ALA 3.5 0.6 - - - +
77B THR* 3.0 9.4 - - - -
78B CYS* 2.9 55.6 + - - +
80B TYR* 3.5 41.5 - - + -
90B GLN* 5.5 0.4 - - - +
91B TYR* 1.3 75.4 - - - +
93B ILE* 1.3 65.8 + - - +
107B ILE* 4.1 21.8 - - + -
108B TYR 3.5 2.7 - - - -
109B ILE* 4.4 14.4 - - + -
142B ILE* 4.0 26.4 - - + +
144B VAL* 4.3 1.1 - - + -
187B PHE* 3.9 22.2 - - + -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET* 4.2 16.8 - - + -
31B PHE* 4.1 17.7 - - + -
69B LEU* 3.9 23.3 - - + -
72B LEU* 4.1 17.9 - - + -
75B PRO* 3.7 30.7 - - + -
76B ALA 3.3 3.4 - - - +
77B THR* 4.3 9.9 - - + -
91B TYR 4.6 2.9 - - - +
92B ILE* 1.3 78.6 - - - +
94B HIS* 1.3 62.3 + - - +
106B LYS 4.3 0.2 - - - +
107B ILE* 3.4 4.0 - - - +
108B TYR* 2.8 42.7 + - + +
110B MET* 4.0 21.8 - - + -
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Residues in contact with HIS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PRO* 4.6 0.2 - - - -
76B ALA* 2.8 37.6 + - + +
92B ILE 4.2 0.2 - - - -
93B ILE* 1.3 75.1 - - - +
95B GLY* 1.3 68.8 + - - +
104B SER 5.2 0.7 - - - -
105B ASP* 3.5 15.4 + - - -
106B LYS 3.3 13.2 - - - -
107B ILE* 3.2 37.0 - - + -
108B TYR* 6.1 0.2 - - - -
129B LEU* 5.0 1.3 - - + +
134B PRO* 3.9 24.7 + - + +
135B GLU 4.8 2.0 - - - -
137B ARG* 4.6 10.1 - - + -
140B HIS* 2.8 38.7 + + - +
142B ILE* 4.5 14.6 - - + -
155B LEU* 3.3 22.3 - - + +
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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
------------------------------------------------------------
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