Contacts of the strand formed by residues 119 - 125 (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 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B THR* 4.8 16.8 - - + -
185B VAL* 3.9 23.1 - - + -
80C PRO 5.2 1.1 - - - +
81C GLY* 5.6 4.7 - - - -
117C ARG* 2.9 11.1 + - + +
118C ASP* 1.3 67.6 - - - +
120C ARG* 1.3 56.5 + - - +
140C VAL* 3.9 25.1 - - + +
141C ALA* 3.8 27.4 - - + -
143C ARG* 5.7 3.4 - - + -
164C MET 4.7 1.8 - - - +
165C GLY* 3.9 21.1 - - - -
166C GLY* 4.0 4.3 - - - +
173C ASP 3.0 13.4 + - - +
174C LEU* 3.2 20.7 - - + +
175C LEU* 2.9 23.9 + - - -
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Residues in contact with ARG 120 (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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148B GLU* 2.9 29.9 + - - -
150B ASP* 3.0 43.1 + - - +
151B HIS* 3.5 29.4 + - + +
153B THR 4.6 2.9 + - - +
185B VAL* 3.2 8.6 - - - +
186B THR* 3.0 32.8 + - + -
190B CYS* 3.4 24.0 - - - -
192B GLY 4.4 1.6 + - - -
193B PRO* 3.4 18.2 - - - +
118C ASP 3.4 3.4 + - - -
119C LEU* 1.3 72.3 - - - +
121C ALA* 1.3 57.3 + - - +
158C VAL* 3.3 22.8 - - - +
175C LEU* 3.2 36.8 - - + +
177C VAL* 3.7 14.4 - - + +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B HIS 3.2 19.1 - - - +
185B VAL* 3.7 0.9 - - - +
186B THR* 3.5 7.4 - - - +
119C LEU 3.8 1.0 + - - -
120C ARG* 1.3 73.7 - - - +
122C GLU* 1.3 59.6 + - - +
140C VAL* 3.5 24.9 - - + -
174C LEU* 3.7 12.1 - - + -
175C LEU 2.9 5.3 + - - -
176C LEU* 3.1 19.1 - - + +
177C VAL 2.8 23.8 + - - -
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Residues in contact with GLU 122 (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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184B HIS* 3.1 49.7 + - + +
185B VAL 3.6 0.2 - - - -
186B THR* 3.4 22.5 - - + +
187B SER 3.1 5.5 + - - -
188B ARG* 2.9 44.7 + - - +
189B LYS* 3.0 21.8 + - - +
121C ALA* 1.3 72.5 - - - +
123C LEU* 1.4 62.3 + - - +
177C VAL* 3.0 14.8 - - + +
179C ARG* 3.5 28.7 + - + +
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Residues in contact with LEU 123 (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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181B LEU* 5.1 6.7 - - + -
182B VAL* 3.6 42.4 - - + -
184B HIS* 5.0 0.4 - - - +
121C ALA 4.3 0.2 - - - +
122C GLU* 1.4 74.5 - - - +
124C PRO* 1.4 67.1 - - - +
125C LEU* 3.4 18.4 + - + -
149C ILE* 5.3 2.0 - - + -
159C ILE* 4.5 9.2 - - + -
176C LEU* 3.6 46.9 - - + +
177C VAL 3.1 23.3 + - - +
178C VAL* 3.6 17.0 - - + +
179C ARG* 2.9 26.6 + - - +
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Residues in contact with PRO 124 (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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163B LEU* 5.9 11.9 - - + -
167B ASN* 5.0 5.5 - - - +
182B VAL* 3.5 24.5 - - + +
183B ALA 6.0 0.2 - - - +
184B HIS* 3.6 28.3 - - + +
123C LEU* 1.4 79.4 - - + +
125C LEU* 1.3 58.4 + - - +
179C ARG* 3.2 18.6 - - + +
181C LEU* 4.3 16.8 - - + -
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Residues in contact with LEU 125 (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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167B ASN* 3.5 28.7 - - - +
181B LEU* 4.9 8.3 - - + -
182B VAL* 5.1 4.7 - - + -
123C LEU* 3.4 17.9 + - + +
124C PRO* 1.3 75.3 - - - +
126C THR* 1.3 73.1 + - - +
129C GLU* 3.8 15.9 - - + +
130C ALA* 4.3 9.4 - - - -
133C GLY* 6.0 0.4 - - - -
149C ILE* 5.3 7.2 - - + -
153C VAL* 3.8 27.6 - - + -
159C ILE* 4.9 7.4 - - + -
178C VAL* 3.6 16.8 - - + -
179C ARG 3.1 6.1 + - - -
180C LEU* 3.4 11.5 - - - +
181C LEU* 3.3 26.9 + - - +
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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