Contacts of the strand formed by residues 170 - 179 (chain B) in PDB entry 4G85
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 GLU 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PRO* 3.2 28.2 - - - +
96A VAL* 3.0 19.8 + - - +
97A PHE* 4.6 1.8 - - + -
61B GLY 3.5 4.3 + - - +
62B THR* 3.4 20.7 - - + +
63B ARG 5.2 3.5 + - - +
65B TYR* 5.2 4.9 + - - -
154B LYS* 3.7 24.1 + - + +
155B VAL 3.4 4.3 - - - -
156B TYR* 2.5 50.0 + - + -
168B TYR* 3.7 10.6 - - - +
169B ARG* 1.3 78.8 - - - +
171B PHE* 1.3 65.6 + - - +
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Residues in contact with PHE 171 (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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65B TYR* 4.9 4.9 - - - -
154B LYS* 4.0 3.8 - - - -
155B VAL* 2.9 43.1 + - + +
157B ARG* 3.8 48.2 - - + -
159B ASP* 5.0 2.0 - - - -
168B TYR* 3.0 48.9 - - + -
170B GLU* 1.3 77.8 - - - +
172B TYR* 1.3 73.2 + - - +
173B GLN* 3.3 14.1 + - + -
387B GLU* 4.9 15.0 - - + -
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Residues in contact with TYR 172 (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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93A ASP* 4.4 0.2 + - - -
65B TYR* 3.3 24.3 + + - +
73B ARG* 3.0 47.7 + - - -
77B PHE* 3.7 22.6 - + - -
152B ILE* 3.7 34.8 - - + -
153B ALA* 3.7 18.2 - - - -
154B LYS* 3.6 25.0 - - + +
171B PHE* 1.3 77.5 - - - +
173B GLN* 1.3 61.0 + - - +
384B ILE 4.8 0.2 - - - +
385B GLY* 5.5 0.3 - - - -
386B VAL* 3.2 36.9 + - + +
387B GLU* 4.7 4.5 + - + +
390B PHE* 4.9 2.5 - + + -
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Residues in contact with GLN 173 (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 ASP* 4.6 4.6 + - - -
131B LEU* 3.6 26.7 - - + +
132B THR* 5.7 0.4 + - - -
152B ILE* 3.6 1.4 - - - +
153B ALA 2.8 33.8 + - - +
155B VAL* 3.2 20.4 - - + +
157B ARG* 2.8 31.5 + - - +
171B PHE* 3.3 10.9 + - + -
172B TYR* 1.3 74.2 - - - +
174B CYS* 1.3 65.4 + - - +
175B ASP* 3.0 24.1 + - - +
383B SER* 4.7 13.0 - - - +
384B ILE 4.9 3.8 - - - +
385B GLY* 6.4 0.7 - - - -
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Residues in contact with CYS 174 (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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80B ILE* 3.7 33.2 - - - -
84B PHE* 4.0 8.9 - - - -
151B HIS 3.7 5.8 - - - -
152B ILE* 3.6 26.9 - - + -
173B GLN* 1.3 81.3 - - - +
175B ASP* 1.3 60.4 + - - +
383B SER* 3.5 1.2 - - - -
384B ILE* 3.1 44.0 + - - +
386B VAL* 4.7 13.0 - - + -
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Residues in contact with ASP 175 (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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84B PHE* 4.5 2.3 - - - -
131B LEU* 3.4 26.4 + - - +
132B THR* 5.0 5.0 + - - -
149B ARG* 3.8 16.3 + - - -
150B TYR* 3.2 4.3 - - - +
151B HIS 2.8 34.5 + - - +
173B GLN* 3.0 29.6 + - - -
174B CYS* 1.3 75.2 - - - +
176B PHE* 1.3 59.4 - - - +
177B ASP* 3.9 9.0 - - - +
382B LEU 3.0 17.0 - - - +
383B SER* 3.6 12.5 - - - -
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Residues in contact with PHE 176 (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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84B PHE* 3.4 43.1 - + + -
87B HIS* 4.8 9.2 - - + -
89B ALA* 3.7 29.8 - - + -
148B LYS* 4.1 14.8 - - + -
149B ARG 3.3 9.0 - - - -
150B TYR* 3.8 4.0 - - + +
175B ASP* 1.3 73.4 - - - +
177B ASP* 1.3 69.8 + - - +
178B ILE* 3.7 35.2 - - + -
190B GLU* 5.0 0.7 - - + -
191B CYS* 4.1 11.7 - - - -
194B ILE* 3.6 31.0 - - + -
381B GLY* 3.2 0.2 - - - -
382B LEU* 3.0 32.1 + - + +
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Residues in contact with ASP 177 (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 THR* 5.5 0.2 + - - -
135B PHE* 3.6 15.3 - - + -
147B ILE 3.9 0.7 - - - +
148B LYS* 3.5 4.3 - - - +
149B ARG* 2.6 59.8 + - - +
175B ASP* 3.9 9.9 - - - +
176B PHE* 1.3 98.2 + - - +
178B ILE* 1.3 67.8 + - - +
179B ALA 3.8 0.7 - - - -
363B TYR* 2.1 42.1 + - - -
379B CYS* 3.6 2.5 - - - -
380B VAL 3.5 3.1 - - - -
381B GLY* 3.8 7.2 - - - -
382B LEU 4.2 0.9 + - - -
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Residues in contact with ILE 178 (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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442A TYR* 3.6 30.5 - - + +
147B ILE 3.6 5.2 - - - +
148B LYS* 3.7 13.0 - - + +
176B PHE* 3.7 19.3 - - + -
177B ASP* 1.3 76.7 - - - +
179B ALA* 1.3 59.5 + - - +
180B GLY 3.8 1.6 + - - +
182B PHE* 3.7 28.2 - - + -
187B PRO* 3.7 26.9 - - + +
190B GLU* 3.6 20.2 - - + -
191B CYS* 4.8 1.8 - - - -
362B ARG* 5.3 1.3 + - - +
378B PRO 4.0 0.2 - - - +
379B CYS* 3.6 4.3 - - - -
380B VAL* 2.8 35.7 + - + +
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Residues in contact with ALA 179 (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 PHE* 3.7 13.5 - - + -
139B LEU* 3.8 14.8 - - + -
146B ASN* 3.2 4.7 - - - +
147B ILE* 2.7 59.8 + - + +
177B ASP 3.8 2.0 - - - -
178B ILE* 1.3 74.6 - - - +
180B GLY* 1.3 58.1 + - - +
182B PHE* 4.0 5.9 - - - -
377B VAL* 4.6 6.1 - - + -
378B PRO 3.5 6.5 - - - +
379B CYS* 3.9 10.1 - - + -
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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