Contacts of the strand formed by residues 197 - 203 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU 3.7 1.2 - - - +
111A ASP* 3.6 1.3 - - - -
112A LEU* 2.8 63.0 + - + +
135A LEU 4.7 0.2 + - - -
136A SER* 2.6 30.9 + - - -
137A LEU 3.7 12.3 - - - +
139A SER* 3.4 16.3 + - - +
141A SER* 3.5 30.4 + - - -
159A LEU* 4.1 12.7 - - - +
165A TYR* 4.5 2.0 - - - -
179A ILE* 4.1 13.6 - - - +
194A ARG* 4.8 4.5 - - - +
195A GLY 4.3 3.4 - - - +
196A ARG* 1.3 75.7 - - - +
198A ILE* 1.3 67.9 + - - +
199A SER* 3.4 17.6 + - - -
302A AKG 2.7 41.3 + - - +
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Residues in contact with ILE 198 (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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49A SER* 5.2 8.3 - - - +
52A LEU* 4.2 13.2 - - + -
53A GLU* 4.0 11.9 - - + +
56A LEU* 3.8 23.8 - - + -
109A VAL* 4.1 19.7 - - + -
110A LEU 3.3 6.7 - - - +
111A ASP* 4.3 6.1 - - + -
136A SER* 3.8 0.5 - - - -
137A LEU* 2.7 65.9 + - + +
138A LEU* 3.9 22.0 - - + +
196A ARG* 3.9 20.0 - - - +
197A ARG* 1.3 75.9 - - - +
199A SER* 1.3 63.1 + - - +
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Residues in contact with SER 199 (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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108A HIS 3.7 0.5 - - - +
109A VAL* 3.4 5.9 - - - +
110A LEU* 2.7 57.5 + - - +
112A LEU* 5.7 0.2 - - - +
134A GLY 6.0 0.2 - - - -
135A LEU 3.2 13.2 - - - -
197A ARG* 3.4 19.1 + - - -
198A ILE* 1.3 75.4 - - - +
200A VAL* 1.3 62.6 + - - +
201A ILE* 3.4 6.4 - - - +
302A AKG 2.7 30.0 + - - -
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Residues in contact with VAL 200 (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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48A LEU* 4.8 11.0 - - + -
52A LEU* 3.9 28.3 - - + -
81A TRP* 4.2 11.0 - - + -
89A MSE 3.8 20.5 - - + +
107A VAL* 3.3 27.6 - - + -
108A HIS 3.4 3.6 - - - +
109A VAL* 4.5 3.8 - - + -
133A ALA 4.0 0.3 - - - +
134A GLY* 3.5 2.3 - - - -
135A LEU* 3.0 40.8 + - + +
137A LEU* 4.5 13.9 - - + -
198A ILE* 4.7 0.4 - - + -
199A SER* 1.3 76.7 - - - +
201A ILE* 1.3 59.8 + - - +
202A CYS* 3.9 2.1 + - - -
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Residues in contact with ILE 201 (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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106A SER 5.1 0.3 - - - +
107A VAL* 3.7 5.7 - - - +
108A HIS* 2.6 53.6 + - + +
110A LEU* 4.1 4.3 - - + -
132A ILE* 4.0 17.9 - - + -
133A ALA 3.6 9.2 - - - +
134A GLY* 4.6 3.6 - - - -
165A TYR* 4.3 3.4 - - - +
199A SER* 3.4 35.7 - - - +
200A VAL* 1.3 73.2 - - - +
202A CYS* 1.3 60.8 + - - +
203A ARG* 3.4 39.4 + - + +
302A AKG 3.8 34.1 - - + +
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Residues in contact with CYS 202 (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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89A MSE 3.5 37.2 - - - -
92A VAL* 3.8 16.8 - - + -
93A GLN* 6.6 0.2 - - - -
97A PHE* 3.9 13.2 - - + -
103A LEU* 3.7 21.3 - - + -
107A VAL* 4.0 18.4 - - - +
132A ILE* 3.7 2.8 - - - -
133A ALA 3.0 32.9 + - - +
200A VAL 3.9 1.3 + - - -
201A ILE* 1.3 72.6 - - - +
203A ARG* 1.3 61.5 + - - +
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Residues in contact with ARG 203 (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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97A PHE* 4.0 4.0 - - - -
103A LEU* 3.8 5.1 - - - +
104A LEU* 3.1 42.6 + - + +
108A HIS* 3.4 22.0 + - - +
123A ASP* 3.1 19.5 + - - -
128A CYS* 3.7 22.9 - - - -
131A THR 3.7 4.0 - - - -
132A ILE* 4.5 5.2 - - + -
201A ILE* 3.4 26.2 + - + +
202A CYS* 1.3 78.3 - - - +
204A SER* 1.3 60.0 + - - +
302A AKG 3.0 40.0 + - - -
66B TRP* 3.2 58.6 - - - +
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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