Contacts of the strand formed by residues 176 - 185 (chain A) in PDB entry 5GGR
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 TYR 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A THR* 5.8 2.3 - - - +
110A THR* 4.1 20.6 + - - +
144A ASP 3.2 8.0 + - - -
145A TYR* 2.9 50.0 + + + +
146A PHE* 3.5 33.6 - + - -
147A PRO* 4.3 0.9 - - + -
148A GLU* 3.8 46.8 - - + +
168A ALA* 4.3 3.8 - - + -
169A VAL 3.6 5.4 - - - +
170A LEU* 3.9 36.4 - - + +
174A GLY 5.2 1.3 - - - -
175A LEU* 1.3 72.2 - - - +
177A SER* 1.3 70.4 + - - +
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Residues in contact with SER 177 (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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141A LEU* 5.6 3.1 - - - -
142A VAL 3.4 11.0 - - - -
143A LYS* 3.1 12.3 - - - +
144A ASP 3.0 11.1 + - - -
145A TYR* 4.0 2.0 - - - -
168A ALA* 4.1 2.7 - - - -
169A VAL* 3.0 38.6 + - - +
171A GLN* 2.5 38.3 + - - -
176A TYR* 1.3 77.7 + - - +
178A LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 178 (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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141A LEU* 3.4 8.4 - - - +
142A VAL* 2.9 50.3 + - + +
145A TYR* 3.7 1.7 - - + +
148A GLU* 6.0 0.7 - - + -
150A VAL* 3.6 28.7 - - + +
152A VAL* 4.6 5.2 - - + -
165A THR* 4.0 17.9 - - + -
166A PHE 3.7 16.2 - - - +
167A PRO 4.4 1.6 - - - +
168A ALA* 3.5 30.5 - - + +
177A SER* 1.3 75.8 - - - +
179A SER* 1.3 91.2 + - - +
180A SER* 3.9 5.6 - - - +
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Residues in contact with SER 179 (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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124A LEU* 4.7 13.2 - - - -
140A CYS 3.4 7.6 - - - -
141A LEU* 3.4 19.3 - - - +
166A PHE* 3.2 37.1 + - - +
178A LEU* 1.3 82.8 - - - +
180A SER* 1.3 60.6 + - - +
181A VAL* 4.1 4.7 - - - -
133B VAL* 4.5 6.2 - - - +
176B SER* 4.2 15.8 + - - -
178B THR* 4.1 12.3 + - - -
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Residues in contact with SER 180 (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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139A GLY* 3.2 0.7 - - - -
140A CYS* 2.5 45.6 + - - -
142A VAL* 5.7 1.1 - - - -
152A VAL* 3.6 20.9 - - - +
154A TRP* 3.0 25.8 + - - -
163A VAL* 4.7 0.3 - - - +
164A HIS 3.5 5.0 + - - -
165A THR* 2.9 29.3 + - - +
178A LEU* 3.9 5.0 - - - +
179A SER* 1.3 73.7 - - - +
181A VAL* 1.3 58.1 + - - +
196A CYS* 5.7 0.2 - - - -
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Residues in contact with VAL 181 (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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124A LEU* 4.4 11.0 - - + -
138A LEU 4.3 1.6 - - - +
139A GLY* 3.6 22.2 - - - +
154A TRP* 4.6 2.5 - - - -
162A GLY 3.7 0.3 - - - +
163A VAL* 3.7 2.6 - - - +
164A HIS* 2.7 56.0 + - + +
166A PHE* 3.8 24.7 - - + -
179A SER* 4.9 4.5 - - - -
180A SER* 1.3 79.7 - - - +
182A VAL* 1.3 60.5 + - - +
118B PHE* 5.0 2.0 - - + -
133B VAL* 5.7 2.5 - - + -
135B LEU* 3.8 34.3 - - + -
137B ASN* 4.3 5.6 - - - +
176B SER* 6.0 0.2 - - - -
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Residues in contact with VAL 182 (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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136A ALA 3.9 0.9 - - - +
137A ALA* 3.7 1.4 - - - -
138A LEU* 3.0 49.2 + - + +
154A TRP* 3.7 32.5 - - + -
159A LEU* 3.9 25.1 - - + -
161A SER 4.1 2.0 - - - +
162A GLY 3.2 8.3 - - - +
163A VAL* 3.7 26.9 - - + -
181A VAL* 1.3 76.7 - - - +
183A THR* 1.3 73.3 + - - +
184A VAL* 4.0 5.1 + - + -
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Residues in contact with THR 183 (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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135A THR* 3.9 17.9 - - + +
136A ALA 3.5 2.9 - - - -
137A ALA* 4.3 13.5 - - + -
161A SER 3.5 14.7 - - - +
162A GLY* 2.9 26.4 + - - +
182A VAL* 1.3 74.5 - - - +
184A VAL* 1.3 69.1 + - - +
116B PHE* 5.5 3.1 - - + -
135B LEU* 5.4 0.2 - - + -
137B ASN* 3.4 34.1 - - + +
138B ASN* 5.8 0.9 - - - +
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Residues in contact with VAL 184 (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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135A THR* 2.9 5.5 + - - -
136A ALA 2.4 50.1 + - - +
138A LEU* 3.6 23.6 - - + -
159A LEU* 4.4 9.4 - - + -
182A VAL* 4.2 18.4 - - + -
183A THR* 1.3 80.3 - - - +
185A PRO* 1.3 70.5 - - + +
189A LEU* 4.1 6.3 - - + -
194A TYR* 3.3 42.4 - - + +
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Residues in contact with PRO 185 (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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134A GLY 4.1 8.5 - - - +
135A THR* 4.3 2.2 - - - +
136A ALA* 4.6 0.4 - - - -
184A VAL* 1.3 93.0 - - + +
186A SER* 1.3 65.1 + - - +
187A SER* 4.6 8.7 - - - +
188A SER* 2.3 47.5 + - - +
189A LEU* 4.0 1.6 + - - +
194A TYR* 4.9 0.9 - - - +
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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