Contacts of the strand formed by residues 117 - 125 (chain C) in PDB entry 6QPA
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 PRO 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C ALA* 3.5 2.8 - - - -
10C ILE 3.1 39.8 + - - +
12C MET* 4.2 15.0 - - + -
115C TRP* 3.3 29.2 - - + +
116C GLU* 1.3 89.3 - - - +
118C TYR* 1.3 59.8 + - - +
119C PHE* 3.7 22.4 - - + -
201C GLN* 3.8 23.6 - - - +
203C GLY 3.2 13.0 - - - +
204C VAL* 3.9 4.9 - - + -
252C GLN* 5.0 0.4 - - - +
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Residues in contact with TYR 118 (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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7C ILE* 3.8 18.8 - - + -
8C ILE 3.6 2.0 - - - -
9C ALA* 4.2 13.7 - - + -
82C TRP* 5.6 1.1 - + + -
85C VAL* 3.7 24.4 - - + +
88C HIS* 2.8 37.5 + + + +
89C GLU* 2.4 40.5 + - - +
117C PRO* 1.3 72.9 - - - +
119C PHE* 1.3 61.5 + - - +
201C GLN* 3.3 6.6 - - - +
202C PHE* 3.0 44.2 + - + -
203C GLY 2.7 12.8 + - - +
204C VAL 3.9 2.2 - - - -
205C SER* 3.6 23.6 - - - -
243C PRO* 3.5 25.8 - - + -
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Residues in contact with PHE 119 (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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7C ILE* 3.7 4.9 - - - -
8C ILE* 2.8 45.6 + - + +
10C ILE* 3.7 29.2 - - + -
12C MET* 4.0 4.5 - - + -
117C PRO* 3.7 29.4 - - + -
118C TYR* 1.3 76.8 - - - +
120C GLU* 1.3 61.0 + - - +
121C VAL 4.0 0.3 + - - -
199C MET* 3.8 28.7 - - + -
200C LYS 3.2 5.8 - - - -
201C GLN* 3.4 35.4 - - + -
202C PHE* 3.4 9.6 - - - -
252C GLN* 3.6 19.7 - - - -
254C LEU* 3.6 28.7 - - + -
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Residues in contact with GLU 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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5C ASN* 4.6 11.0 + - - +
7C ILE* 4.7 8.5 - - + -
119C PHE* 1.3 74.3 - - - +
121C VAL* 1.3 72.9 + - - +
122C VAL* 3.2 18.6 + - - +
199C MET* 3.2 4.1 - - - -
200C LYS* 2.8 55.8 + - + +
202C PHE* 3.5 17.6 - - + +
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Residues in contact with VAL 121 (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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5C ASN* 3.4 35.6 + - - +
6C PRO* 3.9 19.0 + - + +
8C ILE* 3.7 32.3 - - + -
119C PHE 5.6 0.2 - - - -
120C GLU* 1.3 75.1 - - - +
122C VAL* 1.3 61.7 + - - +
123C LYS* 4.1 5.6 - - - +
124C SER* 4.1 18.8 - - - +
197C MET* 3.8 27.6 - - + -
198C ILE 3.6 3.4 - - - -
199C MET* 4.7 2.2 - - + +
312C LEU* 4.5 13.9 - - + -
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Residues in contact with VAL 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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5C ASN* 5.4 1.0 + - - -
120C GLU* 3.2 14.3 + - - +
121C VAL* 1.3 74.2 - - - +
123C LYS* 1.3 67.5 + - + +
176C GLU* 3.4 43.1 - - + +
180C THR* 5.7 1.1 - - - +
198C ILE* 2.7 28.1 + - + +
200C LYS* 3.7 31.9 - - + -
253C TYR* 4.2 5.6 - - + -
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Residues in contact with LYS 123 (chain C).
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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121C VAL* 3.4 4.8 - - - +
122C VAL* 1.3 84.4 - - + +
124C SER* 1.3 67.5 + - - +
180C THR* 4.4 21.8 - - + +
184C GLU* 3.4 24.0 + - - -
196C TRP* 3.3 20.5 - - + -
198C ILE* 2.8 33.5 + - + +
313C LYS* 6.2 3.3 - - - +
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Residues in contact with SER 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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121C VAL* 4.1 12.6 - - - +
123C LYS* 1.3 85.7 + - - +
125C ASP* 1.3 62.6 + - - +
126C LEU* 4.5 3.1 + - - -
196C TRP* 3.4 21.3 - - - -
197C MET* 4.0 12.3 - - - -
312C LEU* 3.8 31.4 - - - +
313C LYS* 4.3 22.4 + - - +
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Residues in contact with ASP 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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124C SER* 1.3 73.7 - - - +
126C LEU* 1.3 59.6 + - - +
127C PRO* 3.8 1.6 - - - +
187C LYS* 3.2 34.8 + - - +
195C GLY* 3.1 9.9 - - - -
196C TRP* 2.8 51.0 + - + +
313C LYS* 5.8 2.5 - - - -
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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