Contacts of the strand formed by residues 197 - 203 (chain B) in PDB entry 4QKB
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 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU 3.6 1.6 - - - +
111B ASP* 3.4 2.2 - - - -
112B LEU* 2.7 67.4 + - + +
136B SER* 2.9 29.7 + - - -
137B LEU 3.8 12.8 - - - +
139B SER* 3.7 16.1 + - - +
141B SER* 3.4 31.4 + - - -
159B LEU* 3.9 13.3 + - - +
165B TYR* 4.2 1.4 - - - -
179B ILE* 4.2 8.9 - - - +
194B ARG* 4.5 7.9 - - - +
195B GLY 3.6 4.0 + - - +
196B ARG* 1.3 76.0 - - - +
198B ILE* 1.3 67.7 + - - +
199B SER* 3.6 16.5 + - - -
302B AKG 3.2 39.2 + - - -
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Residues in contact with ILE 198 (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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49B SER* 4.8 8.1 - - - +
52B LEU* 4.7 5.8 - - + -
53B GLU* 4.3 12.6 - - - +
56B LEU* 3.8 16.2 - - + -
109B VAL* 4.2 16.8 - - + -
110B LEU 3.2 7.0 - - - +
111B ASP* 4.2 5.6 - - + -
136B SER* 3.7 0.7 - - - -
137B LEU* 2.8 63.1 + - + +
138B LEU* 3.8 21.4 - - + +
196B ARG* 3.5 28.7 - - - +
197B ARG* 1.3 76.8 - - - +
199B SER* 1.3 68.6 - - - +
200B VAL* 4.7 2.5 - - + -
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Residues in contact with SER 199 (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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109B VAL* 3.5 4.3 - - - +
110B LEU* 2.7 47.1 + - - +
135B LEU 3.2 11.9 - - - -
165B TYR* 5.9 0.4 - - - -
197B ARG* 3.6 22.4 + - - -
198B ILE* 1.3 75.4 - - - +
200B VAL* 1.3 64.7 - - - +
201B ILE* 3.4 11.7 - - - +
302B AKG 2.7 31.3 + - - -
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.5 15.3 - - + -
52B LEU* 3.8 27.4 - - + -
81B TRP* 4.3 8.7 - - + -
89B MSE 3.8 22.9 - - + +
107B VAL* 3.4 25.8 - - + -
108B HIS 3.5 3.4 - - - +
109B VAL* 4.4 4.7 - - + +
133B ALA 3.6 2.3 - - - +
134B GLY* 3.6 1.7 - - - -
135B LEU* 2.9 44.3 + - + +
137B LEU* 4.6 8.7 - - + -
198B ILE* 4.7 1.3 - - + -
199B SER* 1.3 76.8 - - - +
201B ILE* 1.3 61.4 + - - +
202B CYS* 3.9 0.9 + - - -
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Residues in contact with ILE 201 (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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106B SER 5.1 0.3 - - - +
107B VAL* 3.4 7.1 - - - +
108B HIS* 2.7 55.2 + - - +
110B LEU* 4.3 6.1 - - + -
132B ILE* 3.6 27.1 - - + -
133B ALA 3.5 4.0 - - - +
134B GLY* 4.7 2.0 - - - -
165B TYR* 4.3 4.0 - - - +
199B SER* 3.4 30.1 - - - +
200B VAL* 1.3 77.1 - - - +
202B CYS* 1.3 59.7 + - - +
203B ARG* 3.5 37.2 + - + +
302B AKG 4.2 26.2 - - + +
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Residues in contact with CYS 202 (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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89B MSE 3.1 38.8 - - - -
92B VAL* 4.0 15.0 - - - -
93B GLN* 5.8 1.1 - - - -
97B PHE* 3.5 24.9 - - + -
103B LEU* 4.0 14.4 - - + -
107B VAL* 4.1 11.9 - - - +
132B ILE* 3.5 3.8 - - - +
133B ALA* 2.9 42.1 + - + +
200B VAL 3.9 0.9 + - - -
201B ILE* 1.3 71.7 - - - +
203B ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 203 (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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97B PHE* 4.1 3.6 - - - -
103B LEU* 3.7 9.9 - - - +
104B LEU* 3.2 41.7 + - + +
108B HIS* 3.1 39.0 + - - +
123B ASP* 3.4 17.2 + - - -
128B CYS* 3.8 18.2 - - - -
131B THR 3.6 4.0 - - - -
132B ILE* 4.3 5.6 - - + -
201B ILE* 3.5 23.9 + - + +
202B CYS* 1.3 79.2 - - - +
204B SER* 1.3 60.7 + - - +
302B AKG 3.0 41.4 + - - -
66C TRP* 3.3 46.2 - - - +
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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