Contacts of the strand formed by residues 194 - 203 (chain B) in PDB entry 2JG8
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 ASN 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B LYS* 4.7 14.5 - - + +
133B PHE 3.0 14.1 - - - +
134B THR* 3.9 12.6 + - - +
158B MET 3.9 0.3 - - - +
159B ARG* 3.4 5.2 - - - +
160B GLY* 2.6 46.5 + - - +
161B ARG* 2.4 32.0 + - - +
162B GLU* 5.8 0.2 + - - -
164B ALA* 4.3 1.4 - - - +
192B GLY 4.2 4.2 + - - +
193B GLU* 1.3 73.7 - - - +
195B VAL* 1.3 61.9 + - - +
196B PHE* 3.2 26.5 - - + -
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Residues in contact with VAL 195 (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 PHE* 2.7 40.3 + - + +
143B PHE* 3.9 39.0 - - + -
157B LEU* 4.0 19.1 - - + -
158B MET 3.4 12.8 - - - +
159B ARG* 4.5 4.0 - - + -
187B LEU* 4.2 8.5 - - + -
189B LEU* 3.9 36.6 - - + -
193B GLU 4.4 0.2 + - - -
194B ASN* 1.3 79.4 - - - +
196B PHE* 1.3 65.8 + - - +
215B PHE* 4.3 5.8 - - + -
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Residues in contact with PHE 196 (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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112B THR* 3.9 23.3 - - + -
131B GLY 3.7 9.2 - - - +
132B LYS* 3.5 44.4 - - + -
156B ASN 3.9 0.2 - - - +
157B LEU* 3.9 3.9 - - - +
158B MET* 3.0 56.5 + - + -
164B ALA* 3.7 19.3 - - + -
194B ASN* 3.2 25.8 - - - -
195B VAL* 1.3 83.3 - - - +
197B LEU* 1.3 75.8 + - - +
198B GLN* 4.4 11.7 - - + -
215B PHE* 4.1 10.5 - - - -
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Residues in contact with LEU 197 (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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112B THR* 3.7 5.4 - - - +
113B ILE* 2.8 37.9 + - + +
115B PHE* 3.7 29.2 - - + -
131B GLY 4.8 1.2 + - - -
145B TYR* 3.8 44.6 - - + -
155B VAL* 3.7 19.1 - - + -
156B ASN 3.5 7.4 - - - +
157B LEU* 3.8 30.5 - - + +
196B PHE* 1.3 78.5 - - - +
198B GLN* 1.3 60.7 + - - +
215B PHE* 4.0 18.5 - - + -
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Residues in contact with GLN 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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110B ASP* 3.3 42.0 + - - +
111B GLN 3.5 5.1 - - - +
112B THR* 5.6 0.4 + - - -
113B ILE* 3.9 3.8 - - - -
155B VAL* 3.5 3.9 - - - +
156B ASN* 2.9 57.2 + - + +
158B MET* 3.6 41.3 - - + +
196B PHE* 4.4 10.2 - - + -
197B LEU* 1.3 75.7 - - - +
199B ALA* 1.3 73.9 + - - +
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Residues in contact with ALA 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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107B LEU* 3.7 35.9 - - + -
108B ARG 3.6 18.4 - - - +
110B ASP* 2.8 24.3 + - - +
111B GLN 2.9 13.5 + - - +
113B ILE* 3.6 7.3 - - + +
153B LEU* 6.6 0.9 - - + -
154B CYS 4.5 3.6 - - - -
156B ASN* 4.7 0.2 + - - -
198B GLN* 1.3 80.6 - - - +
200B THR* 1.3 65.2 + - - +
203B ASN* 5.0 3.6 - - + -
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Residues in contact with THR 200 (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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107B LEU 5.1 0.2 - - - +
109B ARG* 3.6 20.6 + - - -
110B ASP* 5.7 0.2 - - - -
154B CYS* 2.9 45.5 + - + +
156B ASN* 3.9 30.5 - - - +
169B THR* 5.2 1.6 - - + -
198B GLN 4.4 0.2 - - - +
199B ALA* 1.3 79.3 - - - +
201B ASP* 1.3 67.1 + - - +
202B LYS* 3.3 13.4 + - - +
203B ASN* 3.7 14.4 - - - +
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Residues in contact with ASP 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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109B ARG* 3.3 31.9 + - - +
200B THR* 1.3 74.1 - - - +
202B LYS* 1.3 81.9 + - + +
203B ASN* 3.1 18.5 + - - +
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Residues in contact with LYS 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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209A GLU* 5.8 1.3 - - - -
152B ASN* 3.5 37.7 - - + +
153B LEU* 3.6 3.5 - - - +
154B CYS* 3.0 45.4 + - + +
173B TYR* 3.4 27.6 + - - +
200B THR* 3.3 14.1 + - - +
201B ASP* 1.3 100.9 + - + +
203B ASN* 1.3 56.7 + - - +
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Residues in contact with ASN 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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106B PRO* 4.4 10.2 - - - +
107B LEU* 2.5 57.3 + - + +
152B ASN 3.5 1.0 + - - -
153B LEU* 4.2 6.7 - - - -
199B ALA* 5.0 1.6 - - + -
200B THR 3.7 13.7 - - - +
201B ASP 3.1 11.9 + - - +
202B LYS* 1.3 73.3 - - - +
204B SER* 1.3 61.8 + - - +
205B LEU* 2.9 13.4 + - - +
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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