Contacts of the strand formed by residues 147 - 154 (chain B) in PDB entry 2KH2
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 LEU 147 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLY 4.0 22.9 - - - +
138B GLY* 5.1 0.2 - - - -
139B GLY* 4.3 15.3 - - - +
140B LEU 5.4 0.2 - - - -
141B VAL* 3.9 32.3 - - + -
146B SER* 1.3 82.1 - - - +
148B ARG* 1.3 63.3 + - - +
149B LEU* 3.9 2.2 - - + -
210B LEU 3.5 1.4 - - - +
211B GLN* 4.0 4.3 + - - -
212B MET* 2.9 48.7 + - - +
215B LEU* 4.4 3.6 - - + +
244B VAL* 3.9 24.0 - - + -
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Residues in contact with ARG 148 (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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137B GLY* 4.2 14.6 - - - +
147B LEU* 1.3 77.4 - - - +
149B LEU* 1.3 69.0 + - - +
150B SER* 3.0 24.5 + - - -
209B TYR* 3.3 35.4 - - + -
210B LEU 3.4 6.3 - - - +
211B GLN* 3.5 21.8 - - - +
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Residues in contact with LEU 149 (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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135B GLU* 6.3 0.2 - - + -
136B SER 3.7 4.9 - - - +
137B GLY 3.6 6.7 - - - +
138B GLY* 3.6 33.0 - - - +
147B LEU* 5.3 3.4 - - + -
148B ARG* 1.3 75.0 - - - +
150B SER* 1.3 62.3 + - - +
165B TRP* 4.6 8.5 - - + -
208B LEU 3.5 0.5 - - - +
209B TYR* 3.5 2.4 - - - -
210B LEU* 2.8 54.0 + - + +
212B MET* 3.6 28.7 - - - -
223B TYR* 3.7 35.4 - - + -
242B THR* 4.6 9.0 - - - +
244B VAL* 4.0 11.7 - - + -
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Residues in contact with SER 150 (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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134B VAL 4.0 1.0 - - - +
135B GLU* 3.2 2.3 - - - +
136B SER* 2.7 45.5 + - - -
137B GLY* 5.9 0.3 - - - -
148B ARG* 3.0 32.1 + - - -
149B LEU* 1.3 77.9 + - - +
151B CYS* 1.3 58.7 + - - +
152B ALA 4.2 0.2 - - - -
165B TRP* 4.6 2.5 - - - -
207B THR* 4.1 9.9 - - - -
208B LEU 3.1 7.9 - - - -
209B TYR* 3.6 9.4 - - - -
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Residues in contact with CYS 151 (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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133B LEU* 3.9 18.6 - - - -
134B VAL 3.7 3.8 - - - -
135B GLU* 3.9 9.2 - - + +
150B SER* 1.3 72.7 - - - +
152B ALA* 1.3 61.9 + - - +
153B ALA* 3.7 0.9 + - - +
165B TRP* 3.7 18.3 - - + -
207B THR* 2.7 21.4 + - - -
208B LEU* 2.9 28.2 + - + +
225B CYS* 2.0 51.8 - - - -
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Residues in contact with ALA 152 (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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132B GLN 3.6 1.9 - - - +
133B LEU* 3.3 9.0 - - - +
134B VAL* 2.9 46.9 + - + +
150B SER 4.2 0.2 - - - -
151B CYS* 1.3 72.2 - - - +
153B ALA* 1.3 60.8 + - - +
154B SER* 4.4 4.0 + - - +
205B LYS 5.9 0.7 - - - +
206B ASN 3.7 6.1 - - - +
207B THR* 3.9 6.1 - - - +
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Residues in contact with ALA 153 (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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133B LEU* 3.6 11.9 - - + -
151B CYS* 3.7 2.8 + - - +
152B ALA* 1.3 70.7 - - - +
154B SER* 1.3 65.5 + - - +
156B PHE* 3.6 26.7 - - + -
158B PHE* 3.8 24.0 - - + -
163B MET* 4.8 2.5 - - + -
206B ASN* 2.9 36.8 + - - +
208B LEU* 5.8 1.1 - - + -
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Residues in contact with SER 154 (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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130B GLU 4.1 0.7 - - - -
132B GLN* 2.9 60.9 + - - +
134B VAL* 5.8 1.6 - - - +
152B ALA* 4.4 5.0 + - - +
153B ALA* 1.3 77.1 - - - +
155B GLY* 1.3 62.5 + - - +
156B PHE* 3.2 16.5 - - - +
206B ASN* 5.9 0.7 - - - +
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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