Contacts of the strand formed by residues 131 - 137 (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 THR 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.5 24.7 + - + +
97A PHE* 3.8 23.1 - - + -
101A GLN* 3.3 22.8 + - - -
128A CYS* 4.3 1.9 - - - -
129A GLY 4.9 0.2 - - - -
130A ALA* 1.3 80.1 - - - +
132A ILE* 1.3 70.4 + - - +
166A ILE* 3.9 20.9 - - + -
167A LEU 3.6 2.7 - - - +
168A ARG* 3.8 14.3 + - + +
203A ARG* 3.7 2.3 - - - -
204A SER* 2.9 32.7 + - - -
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Residues in contact with ILE 132 (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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123A ASP* 3.3 37.7 - - + +
128A CYS* 3.8 16.6 - - - -
131A THR* 1.3 79.2 - - - +
133A ALA* 1.3 62.1 + - - +
165A TYR* 4.1 18.0 - - + +
166A ILE* 3.4 2.9 - - - +
167A LEU* 2.7 49.9 + - + +
172A ARG* 3.6 26.7 - - + +
177A HIS* 4.1 14.1 - - + +
201A ILE* 4.0 24.0 - - + -
202A CYS 3.7 4.5 - - - +
203A ARG* 4.5 1.8 - - + -
302A AKG 6.3 0.9 - - + -
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Residues in contact with ALA 133 (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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92A VAL* 4.3 8.7 - - + -
96A ALA* 3.7 30.5 - - + -
97A PHE* 4.4 5.1 - - + -
131A THR* 4.6 0.6 - - - +
132A ILE* 1.3 79.2 - - - +
134A GLY* 1.3 58.7 + - - +
164A LEU* 4.1 11.0 - - + -
165A TYR* 3.2 10.8 - - - +
166A ILE* 4.0 3.8 - - + -
200A VAL 4.0 0.2 - - - +
201A ILE* 3.6 4.2 - - - +
202A CYS* 3.0 36.9 + - + +
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Residues in contact with GLY 134 (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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133A ALA* 1.3 75.8 - - - +
135A LEU* 1.3 65.0 + - - -
163A SER 3.5 1.0 - - - +
164A LEU* 3.3 7.8 - - - +
165A TYR* 2.9 58.9 + - - -
200A VAL 3.5 8.5 - - - -
201A ILE* 4.5 4.3 - - - -
302A AKG 5.0 0.2 - - - -
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Residues in contact with LEU 135 (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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39A PHE* 3.9 9.4 - - + -
40A LEU* 3.7 39.5 - - + -
48A LEU* 3.9 17.0 - - + -
88A ILE* 3.9 15.9 - - + -
89A MSE 4.2 12.3 - - + -
92A VAL* 4.0 13.7 - - + -
134A GLY* 1.3 73.9 - - - -
136A SER* 1.3 61.7 + - - +
137A LEU* 5.2 2.0 - - + +
163A SER 3.2 9.0 - - - +
164A LEU* 3.8 28.3 - - + -
199A SER* 3.2 9.7 - - - -
200A VAL* 3.0 42.7 + - + +
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Residues in contact with SER 136 (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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135A LEU* 1.3 73.2 - - - +
137A LEU* 1.3 61.6 + - - +
139A SER 5.0 2.2 - - - -
159A LEU* 3.9 19.1 - - - +
160A GLU 4.0 15.9 - - - -
161A PRO* 4.2 2.0 - - - -
162A GLY* 2.8 34.1 + - - -
163A SER* 3.1 14.1 + - - -
165A TYR* 5.0 2.4 - - - -
197A ARG* 2.6 37.9 + - - +
198A ILE 3.8 2.9 - - - -
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Residues in contact with LEU 137 (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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40A LEU* 4.2 12.6 - - + -
45A GLU* 3.9 43.5 - - + +
48A LEU* 3.8 29.2 - - + -
49A SER* 4.6 8.5 - - - +
52A LEU* 4.5 3.1 - - + -
135A LEU* 5.2 2.7 - - + +
136A SER* 1.3 82.8 - - - +
138A LEU* 1.3 70.2 + - + +
139A SER 3.0 11.1 + - - +
161A PRO* 4.4 2.2 - - - -
197A ARG* 3.7 6.4 - - - +
198A ILE* 2.7 55.4 + - + +
200A VAL* 4.5 9.0 - - + -
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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