Contacts of the strand formed by residues 171 - 178 (chain I) in PDB entry 6RAR
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 171 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C OMC 3.3 44.6 - - - +
31C C 3.9 3.8 - - - -
170I GLY* 1.3 76.2 - - - +
172I ARG* 1.3 76.8 + - - +
173I VAL 3.3 0.5 + - - -
192I PHE* 3.7 24.0 - - + -
220I GLU* 3.2 7.2 + - - -
221I VAL* 3.1 43.5 + - + +
226I PHE* 4.6 1.1 - - + -
229I LEU* 3.6 20.4 - - + -
233I VAL* 4.2 11.7 - - + -
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Residues in contact with ARG 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C C 2.9 20.3 + - - +
300D AMP 3.1 43.9 + - - +
145I CYS* 4.0 10.4 - - - +
146I PRO* 2.8 38.0 + - - +
147I LEU* 4.2 4.2 - - - +
171I VAL* 1.3 82.1 - - - +
173I VAL* 1.3 59.7 + - - +
174I LEU* 4.3 9.6 - - + +
185I PHE 3.9 3.0 - - - +
186I SER* 3.9 5.4 - - - -
187I ARG* 4.1 23.0 + - + +
192I PHE* 3.5 10.9 - - - -
218I ASP* 2.6 44.3 + - - -
219I GLY 3.7 8.5 - - - -
220I GLU* 3.6 5.8 + - - -
249I PHE* 4.1 4.8 - - - -
338I TRP* 3.4 19.6 - - - -
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Residues in contact with VAL 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I VAL 3.6 1.6 - - - +
172I ARG* 1.3 77.3 - - - +
174I LEU* 1.3 64.2 + - - +
175I THR* 3.6 21.7 + - - +
184I MET* 3.8 27.6 - - + -
185I PHE 3.5 4.9 - - - +
192I PHE* 4.1 14.8 - - + -
195I PHE* 4.5 3.4 - - + -
217I LEU 3.9 1.6 - - - +
218I ASP* 3.8 2.3 - - - +
219I GLY* 2.9 35.4 + - - +
221I VAL* 3.3 39.0 - - + +
246I LEU* 4.0 15.7 - - + +
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Residues in contact with LEU 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I PHE* 3.7 33.7 - - + -
145I CYS* 3.7 22.4 - - + -
172I ARG* 4.4 5.4 - - + -
173I VAL* 1.3 75.3 - - - +
175I THR* 1.3 61.4 + - - +
176I ILE* 3.9 4.2 + - + -
183I GLU 4.0 0.2 - - - +
184I MET* 3.4 1.4 - - - -
185I PHE* 2.9 36.6 + - - +
186I SER 3.9 10.1 - - - +
187I ARG* 4.1 4.3 - - - -
216I VAL* 4.0 15.0 - - + -
217I LEU 3.6 2.7 - - - -
218I ASP* 3.8 26.0 - - - +
257I PHE* 3.9 19.3 - - + -
330I TYR* 3.9 12.3 - - - +
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Residues in contact with THR 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I VAL* 3.6 18.5 - - - +
174I LEU* 1.3 70.0 - - - +
176I ILE* 1.3 62.0 + - - +
177I ILE* 3.9 2.4 + - + +
182I VAL* 3.4 31.6 - - + -
183I GLU 3.4 5.2 - - - +
184I MET* 3.9 15.7 - - + +
202I ILE* 3.9 17.5 - - + -
215I LEU 3.8 0.9 - - - +
216I VAL* 3.5 2.6 - - - -
217I LEU* 2.8 56.7 + - + +
246I LEU* 3.9 10.7 - - - +
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Residues in contact with ILE 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I PHE* 4.5 18.6 - - + -
174I LEU* 4.3 5.6 - - + +
175I THR* 1.3 74.6 - - - +
177I ILE* 1.3 66.8 + - - +
178I ARG* 3.9 9.8 + - + +
181I LYS 3.5 2.3 - - - +
182I VAL* 3.3 4.2 - - - -
183I GLU* 2.7 38.2 + - + +
185I PHE* 3.5 35.2 - - + -
215I LEU 3.7 4.5 - - - +
216I VAL* 4.2 13.5 - - + +
254I LEU* 4.0 37.7 - - + -
257I PHE* 5.5 2.0 - - + -
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Residues in contact with ILE 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175I THR* 4.7 4.5 - - + +
176I ILE* 1.3 74.8 - - - +
178I ARG* 1.3 61.9 + - - +
179I GLN 4.3 0.2 - - - -
180I ASN* 4.2 10.5 - - - +
181I LYS 3.5 3.4 - - - +
182I VAL* 4.2 15.5 - - + -
202I ILE* 4.1 11.9 - - + -
206I LEU* 3.8 23.3 - - + -
211I ALA* 4.1 22.7 - - + -
214I ASP* 3.2 7.6 - - - +
215I LEU* 2.8 51.2 + - + +
217I LEU* 4.0 26.2 - - + -
276I TRP* 4.0 18.4 - - + -
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Residues in contact with ARG 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I ILE* 3.9 12.8 + - + -
177I ILE* 1.3 74.7 - - - +
179I GLN* 1.3 96.7 + - - +
180I ASN 3.0 0.4 - - - -
181I LYS* 2.9 25.2 + - - +
214I ASP* 3.4 19.8 + - - +
254I LEU* 3.9 18.1 - - + +
258I GLN* 5.4 4.2 - - - +
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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