Contacts of the strand formed by residues 164 - 175 (chain G) in PDB entry 1R8Y
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128G ASP 4.9 0.5 - - - +
129G GLY* 4.2 1.5 - - - -
130G PHE 3.8 5.6 - - - +
133G VAL* 4.0 12.1 - - + -
160G ILE 4.1 2.5 - - - +
161G ALA* 3.1 20.1 + - - +
162G SER 4.0 4.9 - - - +
163G MET* 1.3 75.8 - - - +
165G ARG* 1.3 68.7 + - - +
166G PRO* 4.5 1.4 - - - +
168G GLY* 3.3 35.9 - - - +
169G LEU 3.4 21.8 - - - +
170G LEU* 3.9 18.4 - - + -
258G PHE* 4.4 4.5 - - + -
290G LYS* 3.3 24.6 + - + +
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Residues in contact with ARG 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G HIS 5.0 7.1 + - - -
56G GLY 4.7 10.3 + - - -
57G CYS* 5.3 1.4 - - - +
128G ASP* 3.7 18.2 - - + +
129G GLY* 3.9 8.1 - - - +
130G PHE 3.2 22.9 + - - +
131G ASP* 3.3 37.7 + - - +
164G VAL* 1.3 74.9 - - - +
166G PRO* 1.3 86.9 + - + +
167G GLY* 2.9 31.9 + - - -
168G GLY* 2.8 22.8 + - - -
290G LYS* 3.5 7.2 - - - +
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Residues in contact with PRO 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G ASP* 4.0 19.1 - - - +
164G VAL 4.5 1.6 - - - +
165G ARG* 1.3 112.7 + - + +
167G GLY* 1.3 57.2 + - - +
290G LYS* 3.9 15.2 - - + +
291G THR 4.7 7.2 - - - +
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Residues in contact with GLY 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G ARG* 2.9 19.3 + - - -
166G PRO* 1.3 72.2 - - - +
168G GLY* 1.3 58.9 + - - +
169G LEU* 5.4 0.7 - - - +
289G LYS* 4.2 18.5 + - - +
290G LYS 2.7 23.3 + - - -
291G THR 4.4 1.2 + - - -
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Residues in contact with GLY 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G CYS* 6.2 0.2 - - - -
131G ASP 3.5 11.7 - - - -
164G VAL* 3.3 10.3 - - - +
165G ARG* 2.8 30.8 + - - -
167G GLY* 1.3 75.0 - - - +
169G LEU* 1.3 63.3 + - - +
288G LEU 3.5 0.2 - - - +
289G LYS* 3.4 7.3 - - - -
290G LYS* 3.1 23.2 + - - +
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Residues in contact with LEU 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G LEU* 4.5 13.9 - - + +
52G LEU* 5.0 3.6 - - + -
55G HIS* 3.4 40.2 - - + +
57G CYS* 3.7 18.6 - - - -
131G ASP 3.0 12.6 + - - +
132G ALA* 3.3 10.0 - - + -
133G VAL* 2.7 31.7 + - - -
164G VAL* 3.4 10.8 - - - +
167G GLY 5.4 0.4 - - - +
168G GLY* 1.3 78.8 - - - +
170G LEU* 1.3 55.1 + - - +
171G VAL* 4.1 6.1 - - + -
287G VAL* 4.2 15.5 - - + -
288G LEU 3.1 17.5 - - - +
289G LYS* 3.7 19.3 - - + -
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Residues in contact with LEU 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G VAL* 3.3 27.4 - - + +
134G ILE* 5.1 1.3 - - - -
135G CYS* 5.3 0.4 - - + -
157G LEU* 5.5 1.8 - - + +
160G ILE* 3.3 35.9 - - + -
161G ALA* 4.6 4.3 - - + +
164G VAL* 3.9 6.4 - - + +
168G GLY 4.2 0.2 + - - -
169G LEU* 1.3 73.7 - - - +
171G VAL* 1.3 66.4 + - - +
172G ILE* 4.3 17.5 - - + -
254G VAL* 4.4 16.6 - - + -
258G PHE* 3.9 37.4 - - + -
286G HIS 3.4 1.9 - - - +
287G VAL* 3.3 3.8 - - - +
288G LEU* 2.8 39.3 + - + +
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Residues in contact with VAL 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G TRP* 3.6 31.2 - - + -
48G LEU* 5.1 3.8 - - + -
51G LEU* 3.9 22.7 - - + -
52G LEU* 5.2 4.0 - - + -
132G ALA* 5.6 0.4 - - + -
133G VAL 2.7 13.3 + - - +
134G ILE* 3.3 18.3 - - + +
135G CYS* 2.9 26.9 + - - +
136G LEU* 3.9 9.5 - - + +
169G LEU* 4.7 11.0 - - + -
170G LEU* 1.3 77.3 - - - +
172G ILE* 1.3 60.8 + - - +
285G ILE* 3.8 13.9 - - + -
286G HIS 3.3 3.6 - - - +
287G VAL* 4.5 8.1 - - + -
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Residues in contact with ILE 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G CYS* 3.4 37.2 - - + +
136G LEU* 4.6 1.3 - - - -
140G PHE* 4.2 12.3 - - + -
157G LEU* 4.0 25.1 - - + -
160G ILE* 5.0 12.3 - - + -
170G LEU* 4.3 11.4 - - + -
171G VAL* 1.3 74.8 - - - +
173G ASP* 1.3 66.8 + - - +
250G PHE* 3.8 24.9 - - + -
254G VAL* 4.1 15.3 - - + -
286G HIS* 2.8 44.8 + - + +
288G LEU* 4.7 0.9 - - + -
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Residues in contact with ASP 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G CYS 3.3 4.5 + - - +
136G LEU* 3.4 12.3 - - + +
137G GLY 3.0 19.4 + - - -
138G ASN* 2.9 24.9 + - - -
139G SER 4.5 0.3 + - - -
140G PHE* 4.8 9.2 + - - +
172G ILE* 1.3 82.0 - - - +
174G HIS* 1.3 70.3 + - - +
193G TYR* 2.5 36.0 + - - +
250G PHE* 5.0 1.7 - - - -
283G TYR* 3.6 6.9 - - + -
284G PHE 3.2 15.0 - - - +
285G ILE* 3.9 9.2 - - + -
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Residues in contact with HIS 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G ASN* 3.0 15.5 - - - +
140G PHE* 6.1 1.1 - - + -
141G ALA* 5.3 3.8 - - + +
173G ASP* 1.3 78.8 - - - +
175G ARG* 1.3 78.5 + - - +
177G TYR* 5.0 2.0 - - + -
178G ASP* 5.0 0.7 - - - -
245G HIS* 3.7 31.6 + - + +
246G CYS 4.7 0.4 - - - -
247G LEU* 4.2 13.0 - - - +
250G PHE* 3.5 30.3 - + + +
283G TYR* 4.4 5.2 - - - -
284G PHE* 2.8 58.1 + + + +
286G HIS* 3.0 34.4 + + - -
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Residues in contact with ARG 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G ASN* 2.8 31.8 + - + +
174G HIS* 1.3 93.6 + - - +
176G ASN* 1.3 62.7 + - - +
177G TYR* 2.8 29.2 + - + -
180G ILE* 4.0 19.7 - - + +
186G ALA* 3.6 7.7 + - - +
187G PRO* 2.6 48.3 + - - +
190G LYS* 5.0 8.3 - - - +
200G LYS* 5.5 6.0 - - - +
202G ILE* 5.9 1.0 - - - +
218G LEU* 4.4 19.2 - - - +
220G TYR* 5.1 3.8 + - - -
242G TYR* 6.1 1.2 - - - -
282G CYS* 3.5 13.9 + - - +
283G TYR* 4.2 29.9 + - + +
7282G BME 4.2 5.9 + - - +
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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