Contacts of the strand formed by residues 173 - 182 (chain B) 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 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A HIS* 5.7 1.1 - - - -
103B LYS* 3.3 24.6 + - - -
105B GLU* 3.1 26.8 + - - -
138B ASN* 3.2 16.1 + - - -
139B PHE* 3.0 31.6 + - + +
140B TYR* 4.8 5.2 - + - -
141B PRO 4.7 2.2 - - - -
142B ARG* 3.4 46.5 + - + -
163B VAL* 3.8 14.4 - - + -
164B THR* 3.2 21.3 - - - -
165B GLU* 3.9 2.0 - - - -
166B GLN* 3.1 53.2 + - + -
172B THR* 1.3 75.2 - - - +
174B SER* 1.3 67.7 + - - +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A HIS* 3.1 18.3 - - - -
166A PHE* 3.1 15.9 - - - -
136B LEU 3.3 8.5 - - - -
137B ASN* 2.7 26.5 + - - -
138B ASN 3.2 5.7 + - - -
139B PHE* 3.6 2.2 - - - -
163B VAL* 3.1 5.5 - - - -
164B THR* 2.9 43.0 + - - -
173B TYR* 1.3 79.2 + - - +
175B LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 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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166A PHE* 3.6 2.8 - - - -
135B LEU* 3.7 0.5 - - - -
136B LEU* 2.8 60.6 + - + +
139B PHE* 3.7 13.7 - - + -
142B ARG 5.4 2.2 - - - +
144B ALA* 4.3 21.3 - - + +
146B VAL* 4.4 3.8 - - + -
161B GLU* 3.2 36.1 - - + +
162B SER 3.1 10.1 - - - +
163B VAL* 3.6 21.1 - - + -
174B SER* 1.3 73.8 - - - +
176B SER* 1.3 65.1 + - - +
177B SER* 3.8 19.7 - - - +
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 3.4 38.6 - - - +
179A SER* 4.2 13.2 + - - -
181A VAL* 6.0 0.4 - - - -
133B VAL* 4.4 13.8 - - - +
134B CYS 3.5 7.0 - - - -
135B LEU* 4.7 3.6 - - - -
160B GLN 3.9 1.4 - - - +
161B GLU 3.8 1.6 - - - -
162B SER* 2.9 30.5 + - - -
175B LEU* 1.3 77.7 - - - +
177B SER* 1.3 59.0 + - - +
178B THR* 3.9 4.3 + - - -
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Residues in contact with SER 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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133B VAL* 3.5 2.0 - - - -
134B CYS* 2.8 40.6 + - - -
146B VAL* 3.9 28.0 - - - +
148B TRP* 3.3 27.1 + - - -
159B SER* 3.8 11.3 - - - -
160B GLN 3.7 7.3 + - - -
161B GLU* 4.1 10.4 - - - +
175B LEU* 3.8 5.8 - - - +
176B SER* 1.3 72.5 - - - +
178B THR* 1.3 61.0 + - - +
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Residues in contact with THR 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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141A LEU* 5.1 7.1 - - + +
143A LYS* 5.5 1.1 - - - +
179A SER* 4.1 10.7 + - - -
131B SER* 4.1 15.0 - - - -
132B VAL 3.3 8.5 - - - +
133B VAL* 3.9 17.4 - - + +
148B TRP* 4.4 2.0 - - - -
159B SER* 3.2 26.0 - - - -
160B GLN* 3.3 14.8 + - - -
176B SER* 4.5 5.4 + - - -
177B SER* 1.3 75.5 - - - +
179B LEU* 1.3 63.5 + - - +
180B THR* 3.8 20.0 + - - +
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Residues in contact with LEU 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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130B ALA 3.6 1.2 - - - +
131B SER* 3.2 2.1 - - - -
132B VAL* 2.6 56.8 + - + +
148B TRP* 3.7 56.1 - - + -
150B VAL* 4.8 7.2 - - + -
155B GLN* 5.2 3.6 - - + +
158B ASN* 3.6 26.5 - - + +
159B SER* 4.5 0.9 - - - +
178B THR* 1.3 74.0 - - - +
180B THR* 1.3 59.8 + - - +
181B LEU* 3.6 30.2 + - + +
192B TYR* 4.6 14.4 - - + -
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Residues in contact with THR 180 (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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143A LYS* 5.2 6.5 + - + +
171A GLN* 5.2 9.1 + - - +
129B THR* 3.6 23.1 - - + -
130B ALA 3.1 10.5 - - - +
131B SER* 3.3 15.6 + - - +
158B ASN* 4.2 15.7 + - - +
178B THR* 3.8 12.9 + - - +
179B LEU* 1.3 72.5 - - - +
181B LEU* 1.3 69.7 + - - +
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Residues in contact with LEU 181 (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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129B THR* 3.7 5.6 - - - +
130B ALA* 2.8 31.1 + - + +
132B VAL* 6.4 0.4 - - + -
150B VAL* 5.1 1.8 - - + -
155B GLN* 4.8 12.8 - - - +
158B ASN* 4.1 15.9 - - - +
179B LEU* 3.6 37.8 + - + +
180B THR* 1.3 83.7 - - - +
182B SER* 1.3 71.0 + - - +
185B ASP* 5.1 12.8 - - + +
186B TYR* 4.5 18.8 - - + +
189B HIS* 5.4 3.8 - - + -
192B TYR* 4.3 24.0 - - + +
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Residues in contact with SER 182 (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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128B GLY 4.7 4.0 - - - -
129B THR* 5.0 3.1 - - - +
181B LEU* 1.3 74.0 - - - +
183B LYS* 1.3 67.5 + - - +
184B ALA* 3.0 8.5 + - - +
185B ASP* 3.4 24.1 + - - +
186B TYR* 3.0 20.8 + - - +
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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