Contacts of the strand formed by residues 149 - 154 (chain B) in PDB entry 5GJQ
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 PRO 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG* 3.5 22.0 + - + -
44B GLY 3.3 24.5 - - - +
45B LYS 4.1 16.4 - - - +
46B ASP 5.1 0.2 - - - -
47B CYS 3.3 22.4 - - - +
48B ALA* 4.6 2.2 - - + -
142B GLY 3.8 5.6 - - - +
143B ILE* 3.8 18.8 - - + -
147B GLN 4.1 5.0 - - - +
148B GLY* 1.3 88.2 - - - +
150B GLN* 1.3 69.0 + - - +
222B VAL* 5.2 4.5 - - + -
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Residues in contact with GLN 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 4.4 12.6 - - - +
48B ALA* 4.7 1.5 - - - +
111B VAL* 4.9 9.0 - - + +
112B ASP* 4.8 5.4 + - - +
140B LEU 3.8 0.2 - - - +
141B ILE* 3.1 7.1 - - - +
142B GLY 2.9 40.1 + - - +
144B ASP* 4.0 16.2 - - + +
147B GLN* 3.8 31.4 + - + +
148B GLY 3.8 10.1 - - - +
149B PRO* 1.3 85.5 + - - +
151B VAL* 1.3 66.5 + - - +
152B TYR* 3.4 39.2 + - + -
57C ASP* 5.1 4.2 + - - +
60C SER* 5.8 1.4 - - - -
72b ARG* 5.8 0.7 + - - -
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Residues in contact with VAL 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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41B ALA* 4.2 9.6 - - + +
42B VAL 4.3 5.6 - - - +
43B ARG* 3.8 32.8 - - + +
48B ALA* 4.5 2.9 - - + -
139B ILE* 4.2 16.8 - - + -
140B LEU 3.4 6.5 - - - +
141B ILE* 3.7 15.0 - - + -
150B GLN* 1.3 81.7 + - - +
152B TYR* 1.3 67.5 + - - +
153B LYS* 6.0 0.2 - - + -
162B GLY* 3.3 4.5 - - - -
163B PHE* 2.9 39.9 + - + +
164B LYS 5.1 0.7 - - - +
165B ALA* 5.5 0.2 - - - -
166B THR* 4.0 21.1 - - - +
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Residues in contact with TYR 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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111B VAL* 3.8 28.5 - - + -
112B ASP* 4.0 35.6 + - + +
115B CYS* 4.0 13.0 - - + -
139B ILE* 3.3 8.1 - - - +
140B LEU* 2.8 31.1 + - + +
147B GLN* 5.2 1.6 + - - -
150B GLN* 3.4 38.3 + - + -
151B VAL* 1.3 81.6 - - - +
153B LYS* 1.3 60.9 + - - +
160B TYR* 4.1 20.9 - + - -
161B CYS* 3.2 18.4 - - - -
162B GLY* 3.8 12.1 - - - -
163B PHE* 4.8 0.4 - - - -
60C SER* 3.0 30.7 - - - -
61C VAL* 4.9 0.7 - - + -
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Residues in contact with LYS 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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115B CYS* 3.7 3.4 - - - -
137B CYS* 3.6 23.3 - - - -
138B MET 3.3 12.8 - - - +
139B ILE* 3.7 23.6 - - + -
151B VAL* 6.0 0.2 - - + -
152B TYR* 1.3 79.4 - - - +
154B CYS* 1.3 65.8 + - - +
155B ASP* 4.1 12.6 - - - +
159B TYR 3.8 0.3 - - - +
160B TYR* 3.0 5.0 - - - +
161B CYS* 2.9 28.7 + - - +
163B PHE* 3.6 26.5 - - + -
166B THR* 4.0 12.2 - - + +
167B ALA 3.3 23.7 + - - -
168B ALA* 4.6 1.7 - - - +
172B GLN* 3.6 19.0 - - - +
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Residues in contact with CYS 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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90B GLN* 4.4 5.2 - - - -
115B CYS* 3.5 20.6 - - - -
118B ILE* 4.2 18.6 - - - -
119B ALA* 4.5 11.2 - - + -
122B SER* 6.0 0.4 - - - -
137B CYS* 3.7 9.7 - - - -
138B MET* 3.0 57.7 + - - -
153B LYS* 1.3 75.2 - - - +
155B ASP* 1.3 69.6 + - - +
159B TYR 3.1 9.6 - - - +
160B TYR* 4.0 4.0 - - + -
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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