Contacts of the strand formed by residues 140 - 149 (chain A) in PDB entry 2JK4
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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP* 2.5 54.3 + - - +
135A ASP* 4.0 5.8 + - - -
138A GLY 3.9 0.6 + - - -
139A PRO* 1.3 73.2 - - - +
141A ILE* 1.3 71.9 + - - +
142A ARG* 4.2 2.3 + - - +
159A ASN* 4.2 9.7 + - - -
160A PHE 2.9 18.4 + - - -
161A GLU* 3.8 24.5 - - - +
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Residues in contact with ILE 141 (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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131A ASP 4.2 1.1 - - - -
132A MET* 4.1 21.8 - - + +
134A PHE* 4.7 13.2 - - + -
139A PRO* 4.2 17.0 - - + +
140A SER* 1.3 90.4 - - - +
142A ARG* 1.3 66.7 + - - +
159A ASN* 4.0 0.2 - - - -
160A PHE* 2.7 65.1 + - + +
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Residues in contact with ARG 142 (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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9A THR* 6.1 0.2 - - - +
118A LYS* 4.8 6.1 - - - +
130A CYS* 3.9 11.1 - - - -
131A ASP* 2.7 50.3 + - + +
133A ASP* 5.1 0.6 - - - +
140A SER* 4.2 3.0 + - - +
141A ILE* 1.3 81.0 - - - +
143A GLY* 1.3 86.3 + - - +
144A ALA* 4.7 2.8 - - - +
157A GLN* 3.7 27.1 - - - +
158A MET 3.8 7.9 + - - -
159A ASN* 2.9 39.1 - - - +
160A PHE* 5.4 2.5 - - - -
169A GLN 5.0 3.0 + - - -
171A ASN* 5.5 4.0 - - - +
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Residues in contact with GLY 143 (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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129A GLY* 3.5 12.8 - - - -
131A ASP* 5.3 1.3 - - - +
142A ARG* 1.3 101.3 + - - +
144A ALA* 1.3 62.2 + - - +
157A GLN* 4.1 0.2 - - - -
158A MET* 3.1 30.6 + - - +
160A PHE* 5.9 1.3 - - - -
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Residues in contact with ALA 144 (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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9A THR* 3.6 24.2 - - - +
127A ASN 5.4 0.2 - - - +
128A LEU* 2.8 29.8 - - - +
129A GLY* 3.6 16.4 + - - +
131A ASP* 5.8 2.2 - - - +
142A ARG* 4.7 3.1 - - - +
143A GLY* 1.3 76.8 - - - +
145A LEU* 1.3 63.8 + - - +
146A VAL* 3.6 2.9 - - + -
156A TYR 3.3 10.1 - - - +
157A GLN* 4.4 5.4 - - + +
158A MET* 4.4 4.6 - - - +
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Residues in contact with LEU 145 (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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128A LEU* 3.1 37.2 - - + -
144A ALA* 1.3 75.9 - - - +
146A VAL* 1.3 62.2 + - - +
147A LEU* 3.5 15.4 + - + +
154A ALA 3.9 2.3 - - - +
156A TYR* 2.6 38.2 + - + +
158A MET* 3.7 36.1 - - + -
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Residues in contact with VAL 146 (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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6A VAL 4.9 2.0 - - - +
7A PRO 3.9 10.1 - - - +
8A PRO 3.6 24.7 - - - +
9A THR* 2.8 32.8 - - + +
126A ILE* 2.8 22.4 - - - +
127A ASN* 3.3 22.5 + - - +
128A LEU* 2.8 16.1 - - - +
144A ALA* 4.7 3.8 - - + -
145A LEU* 1.3 71.3 - - - +
147A LEU* 1.3 68.7 + - - +
153A LEU* 5.7 5.4 - - + -
154A ALA 4.1 5.4 - - - +
155A GLY* 4.3 6.7 - - - -
157A GLN* 4.8 5.4 - - - +
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Residues in contact with LEU 147 (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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125A HIS 5.0 0.2 - - - +
126A ILE* 3.0 35.7 - - + -
145A LEU* 3.9 11.4 - - + +
146A VAL* 1.3 80.4 - - - +
148A GLY* 1.3 66.3 + - - +
153A LEU* 3.1 17.3 - - - +
154A ALA* 3.0 39.9 + - + +
156A TYR* 5.2 9.9 - - + -
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Residues in contact with GLY 148 (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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5A ALA 5.2 1.1 - - - -
6A VAL 6.0 0.7 - - - -
125A HIS* 2.6 45.9 + - - +
126A ILE* 3.8 0.8 - - - +
147A LEU* 1.3 79.3 - - - +
149A TYR* 1.3 73.3 + - - +
153A LEU* 3.3 10.3 - - - -
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Residues in contact with TYR 149 (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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125A HIS* 3.5 19.5 + + - +
148A GLY* 1.3 77.7 - - - +
150A GLU* 1.3 62.2 + - + +
151A GLY* 2.6 18.9 + - - -
152A TRP* 2.8 55.2 + + + +
153A LEU* 3.6 4.7 - - - +
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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