Contacts of the strand formed by residues 164 - 175 (chain A) in PDB entry 1D2G
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 VAL 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY* 4.6 0.2 - - - -
130A PHE 3.9 4.7 - - - +
133A VAL* 3.4 24.5 - - + -
160A ILE 4.0 4.9 - - - +
161A ALA* 2.7 19.8 + - - +
162A SER 4.5 2.1 - - - +
163A MET* 1.3 76.0 - - - +
165A ARG* 1.3 64.3 + - - +
168A GLY* 3.4 27.4 - - - +
169A LEU 3.3 24.9 - - - +
170A LEU* 4.0 14.1 - - + -
258A PHE* 4.5 3.1 - - + -
290A LYS* 2.9 43.1 + - + +
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Residues in contact with ARG 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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55A HIS 5.1 5.7 + - - -
56A GLY 5.0 7.1 + - - -
57A CYS* 5.8 1.6 - - - +
128A ASP 3.2 24.2 - - - +
129A GLY* 3.6 12.3 - - - -
130A PHE 3.2 17.9 + - - +
131A ASP* 3.1 35.5 + - - +
163A MET 3.6 3.0 + - - -
164A VAL* 1.3 76.4 - - - +
166A PRO* 1.3 97.3 + - + +
167A GLY* 3.3 21.9 + - - -
168A GLY* 2.8 25.2 + - - -
290A LYS* 3.4 3.8 - - - +
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Residues in contact with PRO 166 (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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128A ASP 4.6 4.3 - - - +
164A VAL 4.4 0.9 - - - +
165A ARG* 1.3 118.2 + - + +
167A GLY* 1.3 51.7 + - - +
290A LYS* 3.8 16.8 - - + +
291A THR 5.2 2.7 - - - +
292A GLY 3.8 22.7 - - - +
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Residues in contact with GLY 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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165A ARG* 3.4 15.8 + - - -
166A PRO* 1.3 72.3 - - - +
168A GLY* 1.3 61.2 + - - +
169A LEU* 4.8 0.9 - - - +
289A LYS* 3.2 31.0 + - - -
290A LYS 2.6 21.4 + - - -
291A THR* 5.0 0.8 + - - +
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Residues in contact with GLY 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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131A ASP 3.1 14.6 - - - -
164A VAL* 3.4 7.9 - - - -
165A ARG* 2.8 25.1 + - - -
166A PRO 3.0 1.2 + - - -
167A GLY* 1.3 82.2 - - - +
169A LEU* 1.3 59.8 + - - -
289A LYS* 3.2 6.1 - - - +
290A LYS 2.7 29.8 + - - -
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Residues in contact with LEU 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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51A LEU* 4.0 27.8 - - + +
52A LEU* 4.9 2.9 - - + -
55A HIS* 3.7 52.9 - - + +
57A CYS* 4.5 8.3 - - - -
131A ASP 2.8 12.3 + - - +
132A ALA* 3.4 8.4 - - + -
133A VAL 3.0 22.9 + - - -
164A VAL* 3.3 12.4 - - - +
167A GLY 4.8 0.4 - - - +
168A GLY* 1.3 79.9 - - - +
170A LEU* 1.3 60.1 + - - +
171A VAL* 4.6 6.1 - - + -
287A VAL* 4.7 10.1 - - + -
288A LEU 3.1 7.9 - - - +
289A LYS* 4.0 21.1 - - + +
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Residues in contact with LEU 170 (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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133A VAL* 3.3 22.0 - - + +
134A ILE* 5.2 1.6 - - - -
135A CYS* 5.5 0.9 - - + +
157A LEU* 5.7 3.1 - - + +
160A ILE* 3.8 30.5 - - + -
161A ALA* 5.0 4.5 - - + +
164A VAL* 4.0 4.9 - - + -
169A LEU* 1.3 76.0 - - - +
171A VAL* 1.3 65.5 + - - +
172A ILE* 4.3 18.4 - - + -
254A VAL* 4.1 19.5 - - + -
258A PHE* 3.6 39.9 - - + -
286A HIS 3.3 4.3 - - - +
287A VAL* 3.3 1.6 - - - -
288A LEU* 2.7 38.6 + - + +
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Residues in contact with VAL 171 (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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47A TRP* 3.5 32.8 - - + -
48A LEU* 5.1 2.2 - - + -
51A LEU* 3.8 22.0 - - + -
52A LEU* 5.4 2.7 - - + -
132A ALA* 5.6 1.1 - - + -
133A VAL 2.9 8.2 + - - +
134A ILE* 3.3 20.7 - - + -
135A CYS* 2.9 26.3 + - - +
136A LEU* 3.7 15.4 - - + +
169A LEU* 4.6 11.0 - - + -
170A LEU* 1.3 79.7 - - - +
172A ILE* 1.3 60.8 + - - +
285A ILE* 3.8 8.7 - - + -
286A HIS 3.4 3.6 - - - +
287A VAL* 4.9 6.5 - - + -
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Residues in contact with ILE 172 (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 CYS* 3.5 28.9 - - + +
136A LEU* 4.5 1.3 - - - -
140A PHE* 4.0 25.8 - - + -
157A LEU* 4.1 11.4 - - + -
160A ILE* 5.1 4.9 - - + -
170A LEU* 4.3 25.4 - - + -
171A VAL* 1.3 76.0 - - - +
173A ASP* 1.3 71.0 + - - +
250A PHE* 3.8 27.6 - - + -
254A VAL* 4.3 5.6 - - + -
285A ILE* 4.6 0.4 - - - -
286A HIS* 2.8 47.4 + - + +
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Residues in contact with ASP 173 (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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135A CYS 3.4 3.2 + - - +
136A LEU* 3.4 9.3 - - + +
137A GLY 3.1 18.2 + - - -
138A ASN* 2.9 29.1 + - - +
139A SER 4.9 0.2 + - - -
140A PHE* 4.6 9.2 - - - +
141A ALA 5.5 0.2 + - - -
172A ILE* 1.3 84.8 - - - +
174A HIS* 1.3 68.3 + - - +
193A TYR* 2.5 26.9 + - - -
250A PHE* 5.0 2.2 - - - -
283A TYR* 3.8 6.2 - - + -
284A PHE 3.1 15.9 - - - +
285A ILE* 3.8 16.6 - - + -
286A HIS* 4.9 0.7 - - - -
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Residues in contact with HIS 174 (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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138A ASN* 3.3 14.1 - - - +
140A PHE* 6.2 0.7 - - + -
141A ALA* 5.5 2.9 - - + +
173A ASP* 1.3 77.0 - - - +
175A LYS* 1.3 86.9 + - - +
177A TYR* 4.9 2.0 - - + -
178A ASP* 5.2 0.2 + - - -
245A HIS* 3.7 31.2 + - + +
247A LEU* 4.0 13.3 + - + -
250A PHE* 3.5 39.4 - + + -
283A TYR* 3.6 5.1 - - - +
284A PHE* 2.7 50.2 + + + -
286A HIS* 3.1 29.6 + + - -
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Residues in contact with LYS 175 (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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138A ASN* 3.0 23.6 + - - +
174A HIS* 1.3 97.4 - - - +
176A ASN* 1.3 59.3 + - - +
177A TYR* 2.8 32.5 + - + +
180A ILE* 4.1 17.9 - - + -
186A ALA* 6.1 3.4 - - + -
187A PRO* 5.3 10.5 - - + -
190A LYS* 5.5 9.4 - - - -
191A ASN 6.1 0.2 - - - +
282A CYS* 3.5 19.7 - - + +
283A TYR* 3.1 41.6 + - + +
284A PHE* 4.4 0.7 - - - -
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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