Contacts of the strand formed by residues 174 - 180 (chain C) in PDB entry 6PSI
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 LEU 174 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C LEU* 3.2 30.3 - - + +
121C ALA* 3.7 23.8 - - + -
138C VAL* 4.4 6.5 - - + -
140C VAL* 3.9 21.8 - - + -
159C ILE 3.5 1.6 - - - +
161C VAL* 2.8 46.1 + - + -
164C MET* 3.4 40.4 - - + +
165C GLY* 3.7 1.6 - - - +
173C ASP* 1.4 75.3 - - - +
175C LEU* 1.3 66.3 + - - +
176C LEU* 3.9 25.1 - - + -
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B HIS* 3.4 22.0 - - + +
148B GLU* 3.3 20.4 - - - +
149B LYS* 4.1 11.4 - - - +
150B ASP 3.8 11.2 - - - +
200B CYS* 4.1 0.2 - - - -
118C ASP* 5.0 2.7 - - + -
119C LEU 2.9 9.9 + - - +
120C ARG* 3.2 44.5 - - + +
121C ALA 2.9 21.9 + - - -
158C VAL* 3.7 16.2 - - + -
159C ILE 3.5 1.6 - - - -
160C ARG* 3.9 13.0 - - - -
172C GLY 4.7 2.7 - - - +
173C ASP* 3.5 13.9 - - - +
174C LEU* 1.3 81.2 - - - +
176C LEU* 1.3 59.7 + - - +
177C VAL* 3.2 6.4 + - - +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 5.5 4.0 - - + -
182B VAL* 5.1 0.7 - - + -
184B HIS 5.6 0.2 - - - +
121C ALA* 3.1 33.4 - - + +
123C LEU* 3.6 34.3 - - + +
138C VAL* 5.0 15.0 - - + -
147C VAL* 5.4 3.8 - - + -
149C ILE* 4.3 26.0 - - + -
157C SER 3.4 1.9 - - - +
158C VAL* 3.4 1.9 - - - -
159C ILE* 2.8 53.0 + - + +
161C VAL* 4.4 9.9 - - + -
174C LEU* 3.9 22.7 - - + -
175C LEU* 1.3 66.3 - - - +
177C VAL* 1.3 62.6 + - - +
178C VAL 3.5 2.0 + - - -
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Residues in contact with VAL 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B THR* 4.7 2.5 - - + -
189B LYS 5.6 0.2 - - - +
190B CYS* 4.0 18.6 - - + -
191B TYR* 5.0 5.6 - - + +
192B GLY 5.7 0.9 - - - +
120C ARG* 3.7 47.1 - - + +
121C ALA 2.8 10.2 + - - +
122C GLU* 3.0 27.8 - - + +
123C LEU* 3.1 4.1 + - - -
156C GLY* 3.3 27.6 - - - +
157C SER 3.4 4.7 - - - -
158C VAL* 3.9 9.9 - - + -
175C LEU 4.0 1.1 - - - +
176C LEU* 1.3 69.0 - - - +
178C VAL* 1.3 63.3 + - - +
179C ARG* 4.5 10.5 - - - +
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C LEU* 3.6 11.7 - - + +
125C LEU* 3.6 34.1 - - + -
153C VAL* 3.5 30.1 - - + -
154C ARG 3.0 34.1 - - - +
155C GLU* 3.9 3.1 - - - +
156C GLY* 3.0 16.3 + - - +
157C SER 3.0 11.4 + - - +
176C LEU 3.5 2.4 + - - +
177C VAL* 1.3 71.3 - - - +
179C ARG* 1.3 80.5 + - - +
180C LEU* 3.7 17.0 - - + -
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Residues in contact with ARG 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LYS* 3.7 23.7 - - - +
191B TYR* 2.8 41.3 + - - -
122C GLU* 3.5 46.6 + - + +
123C LEU 2.9 19.2 + - - +
124C PRO* 3.2 12.4 - - + +
125C LEU 3.1 21.3 + - - -
155C GLU* 2.8 21.9 + - - -
156C GLY* 3.7 2.6 - - - -
177C VAL* 3.8 8.2 - - - +
178C VAL* 1.3 100.7 + - - +
180C LEU* 1.3 65.0 + - - +
181C LEU* 3.8 0.9 + - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ARG* 5.8 1.4 - - - +
125C LEU 3.4 17.7 - - - +
126C THR* 4.4 2.7 - - - -
127C LEU* 3.5 36.1 - - + -
153C VAL* 3.9 11.0 - - + -
154C ARG* 4.2 3.1 - - - -
155C GLU* 3.0 55.2 + - + +
178C VAL* 3.7 18.4 - - + -
179C ARG* 1.3 75.0 - - - +
181C LEU* 1.3 65.4 + - - +
182C PRO* 4.9 0.2 - - - +
183C HIS 5.6 0.2 - - - -
184C PRO* 3.9 26.1 - - + +
186C PHE 4.7 4.0 - - - +
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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