Contacts of the strand formed by residues 159 - 169 (chain A) in PDB entry 2RFQ
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 ARG 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A VAL 3.5 0.3 - - - +
155A ILE* 3.3 6.4 - - - +
156A LYS 2.8 34.9 + - - +
157A ASP* 4.1 5.8 - - + +
158A GLY* 1.3 80.2 - - - +
160A PRO* 1.4 74.4 - - + +
161A VAL* 3.7 6.9 + - + +
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Residues in contact with PRO 160 (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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153A PRO* 3.8 24.7 - - + -
154A VAL 3.1 7.6 - - - +
155A ILE* 4.0 9.6 - - + -
158A GLY 4.8 0.9 - - - +
159A ARG* 1.4 87.6 - - + +
161A VAL* 1.3 62.0 + - - +
162A ASP 3.7 1.3 - - - +
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Residues in contact with VAL 161 (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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154A VAL* 2.9 31.1 + - + +
156A LYS* 3.9 31.2 - - + +
159A ARG* 3.8 14.1 - - + +
160A PRO* 1.3 79.9 - - - +
162A ASP* 1.3 66.9 + - + +
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Residues in contact with ASP 162 (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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153A PRO* 3.3 8.8 - - - +
154A VAL* 3.1 31.5 + - + +
160A PRO* 3.7 1.1 - - - +
161A VAL* 1.3 83.3 + - + +
163A PHE* 1.3 68.2 + - - +
164A VAL* 3.4 15.2 - - + +
206A SER* 2.8 36.6 + - - -
208A LYS* 4.6 6.6 + - - +
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Residues in contact with PHE 163 (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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117A TYR 3.6 22.7 - - - -
119A PRO* 3.7 32.3 - - + -
151A GLY 3.8 1.1 - - - -
152A GLY* 3.6 33.2 - - - -
153A PRO* 4.0 7.6 - - + -
162A ASP* 1.3 83.7 + - - +
164A VAL* 1.3 63.7 - - - +
207A PHE* 3.2 52.0 + + + +
208A LYS 4.7 0.7 + - - -
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Residues in contact with VAL 164 (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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130A TYR* 5.8 0.2 - - - +
150A LEU 3.8 0.2 - - - +
151A GLY* 3.3 4.7 - - - -
152A GLY 2.9 35.4 + - - +
154A VAL* 3.8 17.3 - - + -
162A ASP* 3.4 25.8 - - + +
163A PHE* 1.3 79.4 - - - +
165A SER* 1.3 62.1 + - - +
166A PHE* 3.4 39.7 - - + -
204A VAL* 3.7 17.3 - - + -
205A LEU 3.3 9.6 - - - +
206A SER* 3.8 9.4 - - - +
207A PHE* 3.9 7.9 - - - -
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Residues in contact with SER 165 (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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92A HIS* 3.2 23.1 - - - -
96A PHE* 3.8 13.4 - - - -
117A TYR* 3.7 8.0 - - - -
149A VAL* 4.3 10.1 - - - -
150A LEU 3.4 7.0 - - - -
151A GLY* 4.5 0.3 - - - -
164A VAL* 1.3 73.3 + - - +
166A PHE* 1.3 62.4 + - - +
167A LEU 4.0 0.2 - - - -
204A VAL* 3.4 6.1 - - - +
205A LEU 2.9 31.2 + - - -
207A PHE* 3.2 27.7 - - - -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ALA* 4.3 4.5 - - - -
123A GLY* 3.5 32.3 - - - -
130A TYR* 4.1 17.3 - + + -
132A VAL* 3.7 27.8 - - + -
136A TRP* 4.7 4.5 - + - -
148A ALA 3.3 2.9 - - - +
149A VAL* 3.3 4.0 - - - -
150A LEU* 2.8 47.0 + - + +
152A GLY* 4.0 17.3 - - - -
153A PRO 3.8 7.0 - - - -
154A VAL* 4.3 2.5 - - + -
164A VAL* 3.4 27.1 - - + -
165A SER* 1.3 71.9 - - - +
167A LEU* 1.3 60.0 + - - +
168A ILE* 3.7 20.2 + - + +
199A VAL* 4.5 4.5 - - + -
203A ARG 4.0 2.9 - - - -
204A VAL* 3.7 20.0 - - + -
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Residues in contact with LEU 167 (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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93A LEU* 3.8 20.2 - - + -
96A PHE* 3.8 11.9 - - + -
100A ALA* 3.9 21.1 - - + +
104A VAL* 3.8 24.0 - - + -
113A ILE* 4.6 4.0 - - + -
147A TRP* 3.6 36.1 - - + -
148A ALA 3.4 7.2 - - - +
149A VAL* 3.8 20.4 - - + -
165A SER 3.8 1.0 + - - -
166A PHE* 1.3 70.5 - - - +
168A ILE* 1.3 60.9 - - - +
169A PRO* 4.5 0.3 - - - +
199A VAL* 3.8 6.1 - - - +
203A ARG* 2.9 49.6 + - + +
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Residues in contact with ILE 168 (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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132A VAL* 4.2 10.3 - - + -
147A TRP* 3.3 5.1 - - - -
148A ALA 2.8 33.8 + - - +
150A LEU* 4.0 18.2 - - + -
166A PHE* 3.9 13.0 - - + +
167A LEU* 1.3 80.3 - - - +
169A PRO* 1.4 81.1 - - + +
172A ASP* 3.7 18.6 - - + +
173A TYR* 3.3 16.3 - - + -
194A VAL* 3.9 24.7 - - + -
197A VAL* 4.2 7.0 - - + -
199A VAL* 3.6 27.1 - - + -
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Residues in contact with PRO 169 (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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146A SER 3.7 4.0 - - - +
147A TRP* 3.4 39.5 - - + -
168A ILE* 1.4 90.9 - - + +
170A ARG* 1.3 60.7 + - - +
171A GLU* 4.0 22.7 - - + +
172A ASP* 2.9 40.8 + - - +
173A TYR* 3.3 10.0 - - - -
199A VAL* 6.4 0.2 - - + -
203A ARG* 4.0 14.6 - - - +
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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