Contacts of the strand formed by residues 153 - 163 (chain B) in PDB entry 1RGQ
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 ALA 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ILE* 4.1 25.8 - - + -
97B LEU* 4.3 15.7 - - + +
98B THR 3.2 14.8 + - - +
99B PRO* 4.6 1.8 - - + -
100B CYS* 2.9 23.9 + - - +
145B PRO* 5.5 2.7 - - + -
146B LEU 3.7 6.3 - - - +
147B LEU* 4.1 5.0 - - + +
151B GLY 4.2 0.2 + - - -
152B HIS* 1.3 69.2 - - - +
154B VAL* 1.3 60.3 + - - +
155B GLY 4.8 2.5 - - - +
175B VAL* 3.4 23.6 - - + +
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Residues in contact with VAL 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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100B CYS* 4.0 12.1 - - + -
104B SER 5.3 1.3 - - - +
107B LEU* 3.7 37.0 - - + -
121B ARG* 3.7 30.1 - - - +
146B LEU* 2.8 12.7 + - + +
147B LEU 4.0 0.2 - - - -
148B CYS* 3.7 34.5 - - + +
153B ALA* 1.3 75.8 - - - +
155B GLY* 1.3 59.2 + - - +
172B PHE* 4.6 3.5 - - + -
174B PRO* 3.6 6.4 - - - +
175B VAL* 3.0 28.7 + - + +
176B GLU* 4.4 1.1 - - - +
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Residues in contact with GLY 155 (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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51B ILE* 6.0 0.4 - - - +
145B PRO* 3.5 4.3 - - - +
146B LEU* 2.7 39.4 + - - +
153B ALA* 3.6 3.1 - - - +
154B VAL* 1.3 83.3 - - - +
156B LEU* 1.3 66.7 + - - -
172B PHE* 4.3 6.7 - - - -
173B ILE 3.2 13.0 - - - -
174B PRO* 4.1 2.5 - - - -
175B VAL* 4.2 4.6 - - - +
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Residues in contact with LEU 156 (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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49B THR* 4.5 6.5 - - - +
51B ILE* 3.7 28.0 - - + -
56B TRP* 3.8 34.3 - - + +
57B THR* 4.2 6.5 - - - +
58B VAL* 6.1 0.4 - - + -
85B LEU* 4.7 8.3 - - + -
143B GLY* 3.9 22.9 - - - +
144B GLY 3.2 7.0 - - - +
145B PRO* 5.3 0.4 - - + -
155B GLY* 1.3 77.9 - - - +
157B PHE* 1.3 64.1 + - - +
158B ARG 3.4 0.3 + - - -
172B PHE* 3.3 5.1 - - - +
173B ILE* 2.9 51.6 + - + +
175B VAL* 5.4 1.1 - - + -
178B LEU* 4.1 19.5 - - + -
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Residues in contact with PHE 157 (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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58B VAL* 4.2 4.2 - - - +
109B LEU* 3.8 29.2 - - + -
110B VAL 6.0 0.2 - - - +
138B LEU* 3.7 46.7 - - + -
141B SER* 3.3 29.4 - - - +
142B SER* 3.5 6.2 - - - -
143B GLY* 2.8 27.2 + - - -
144B GLY 2.8 18.6 + - - +
146B LEU* 3.7 7.3 - - + +
156B LEU* 1.3 69.5 - - - +
158B ARG* 1.3 60.5 + - - +
159B ALA 3.3 26.0 - - - -
160B ALA* 4.1 4.3 - - + -
170B VAL* 3.7 21.3 - - + -
171B ASP 3.9 7.6 - - - -
172B PHE* 4.4 0.4 - - + -
194B AKP 3.8 21.3 - - + -
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Residues in contact with ARG 158 (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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58B VAL* 4.3 7.0 - - + -
60B HIS* 3.5 24.2 - - + -
82B ASP 5.8 1.2 + - - -
83B GLN 4.9 0.8 + - - -
84B ASP* 2.9 39.1 + - - +
156B LEU 3.4 0.8 + - - -
157B PHE* 1.3 76.0 - - - +
159B ALA* 1.3 61.2 + - + +
171B ASP* 3.0 41.1 + - - +
172B PHE* 4.2 2.5 - - - -
173B ILE* 4.0 27.8 - - + -
194B AKP 3.5 59.8 + - - +
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Residues in contact with ALA 159 (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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157B PHE* 3.3 11.2 - - - -
158B ARG* 1.3 85.3 - - - +
160B ALA* 1.3 57.8 + - - +
171B ASP* 2.6 46.9 + - + +
194B AKP 3.2 52.5 - - + +
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Residues in contact with ALA 160 (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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138B LEU* 4.8 3.8 - - + -
157B PHE* 4.1 15.5 - - + -
159B ALA* 1.3 75.3 - - - +
161B VAL* 1.3 62.0 + - - +
162B CYS* 3.4 8.7 - - - -
167B THR* 3.8 27.8 - - + -
169B ALA 3.7 5.2 - - - +
170B VAL* 4.5 2.2 - - + +
194B AKP 3.2 47.8 + - + +
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Residues in contact with VAL 161 (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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126B ARG* 3.6 32.1 - - - +
160B ALA* 1.3 69.5 - - - +
162B CYS* 1.3 60.6 + - - +
163B THR* 4.0 13.9 + - + +
166B VAL 3.9 0.5 - - - +
167B THR* 3.3 20.8 - - - -
168B LYS* 3.5 7.3 + - + +
169B ALA* 2.8 35.2 + - + +
170B VAL* 4.6 2.2 - - - +
194B AKP 3.7 31.4 - - + +
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Residues in contact with CYS 162 (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 ILE* 3.5 22.4 - - + -
160B ALA* 3.4 19.5 - - - -
161B VAL* 1.3 70.9 - - - +
163B THR* 1.3 62.9 + - - +
164B ARG 4.1 0.9 + - - -
165B GLY* 5.1 5.4 - - - +
166B VAL 3.5 6.5 - - - +
167B THR* 3.5 25.1 - - + -
194B AKP 3.0 58.3 + - + +
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Residues in contact with THR 163 (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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161B VAL* 4.0 14.1 + - + +
162B CYS* 1.3 76.3 - - - +
164B ARG* 1.3 65.1 + - - +
165B GLY 3.1 3.8 + - - -
166B VAL* 3.0 33.9 + - - +
168B LYS* 3.9 28.1 + - + +
194B AKP 5.2 7.9 - - + +
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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