Contacts of the strand formed by residues 120 - 127 (chain C) in PDB entry 1P7L
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 GLY 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C GLN* 1.3 75.3 - - - +
121C LEU* 1.3 58.1 + - - -
122C MET* 3.9 9.1 - - - +
270C VAL* 6.3 0.4 - - - -
271C ASP* 5.4 3.8 - - - -
299C SER* 2.9 4.0 - - - -
300C TYR* 2.6 33.7 + - - -
8D GLU* 4.2 14.8 - - - -
167D GLN* 2.5 25.8 + - - +
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Residues in contact with LEU 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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120C GLY* 1.3 73.9 - - - +
122C MET* 1.3 69.1 + - - +
123C PHE* 4.1 20.2 - - + -
258C GLY* 3.4 32.4 - - - +
260C GLY 5.2 2.3 + - - -
271C ASP* 5.3 1.4 + - - +
297C GLN* 3.3 15.3 - - + +
298C VAL 3.2 10.5 - - - +
299C SER* 3.9 10.5 - - - -
5D PHE* 5.2 0.2 - - + -
6D THR* 2.8 29.2 - - - +
7D SER* 4.0 9.0 - - - -
8D GLU* 3.6 30.7 + - + +
167D GLN* 4.8 1.1 - - - +
247D ILE* 6.0 0.4 - - + -
252D GLY 4.0 13.0 - - - +
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Residues in contact with MET 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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120C GLY* 3.9 7.4 - - - +
121C LEU* 1.3 91.9 - - - +
123C PHE* 1.3 64.7 + - - +
124C GLY 4.2 0.3 + - - -
258C GLY* 4.9 2.9 - - - +
260C GLY* 6.1 0.4 - - - -
270C VAL* 2.8 40.6 - - + +
271C ASP* 3.3 24.0 - - - +
274C ALA* 3.5 10.3 - - + -
275C ALA* 4.1 20.2 - - + -
278C ALA* 5.0 1.4 - - + +
297C GLN* 3.2 7.5 - - - +
298C VAL* 2.7 58.7 + - + +
300C TYR* 4.0 11.7 - - - -
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Residues in contact with PHE 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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121C LEU* 4.1 13.7 - - + -
122C MET* 1.3 77.2 - - - +
124C GLY* 1.3 60.9 + - - +
250C THR* 5.9 1.2 - - - +
251C TYR* 3.9 14.4 + - + -
255C ALA* 5.9 0.2 - - + -
256C ARG* 3.3 42.1 - - + +
257C HIS* 3.3 34.3 - - - +
258C GLY* 3.8 4.8 - - - +
275C ALA* 4.8 8.7 - - - +
278C ALA* 4.1 3.8 - - - +
295C GLU* 3.9 20.2 - - + -
296C ILE 3.3 14.4 - - - -
297C GLN* 3.2 39.3 - - + -
311C MET* 5.2 3.8 - - + -
360C PHE* 5.5 1.2 - - - -
5D PHE* 4.1 5.8 - + - -
253D GLY* 3.6 20.0 - - - -
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Residues in contact with GLY 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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123C PHE* 1.3 73.9 - - - +
125C TYR* 1.3 63.6 + - - +
251C TYR* 3.7 4.3 - - - -
275C ALA 4.8 0.4 - - - -
278C ALA* 3.4 35.6 - - - +
279C ARG 3.9 0.2 - - - -
282C ALA* 4.2 0.9 - - - -
295C GLU* 3.3 9.5 - - - +
296C ILE 2.8 32.8 + - - -
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Residues in contact with TYR 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 GLY* 1.3 74.1 - - - +
126C ALA* 1.3 83.8 + - - +
127C THR* 4.2 10.3 + - + -
135C PRO* 4.0 14.4 - - + -
251C TYR* 3.0 32.8 + + + -
254C MET* 4.0 29.2 + - + +
255C ALA* 3.3 27.8 - - + -
279C ARG* 3.1 26.8 + - - +
282C ALA* 3.7 7.9 - - - +
293C ARG* 3.8 25.2 + - - +
294C CYS 3.6 8.1 - - - -
295C GLU* 3.5 20.6 - - + -
315C PHE* 3.8 26.5 - + - -
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Residues in contact with ALA 126 (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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125C TYR* 1.3 85.0 - - - +
127C THR* 1.3 63.5 + - - +
133C LEU* 3.7 8.3 - - + +
279C ARG* 3.9 2.9 - - - +
282C ALA* 3.3 35.4 - - + +
283C LYS* 3.3 12.1 - - + +
286C VAL* 3.9 9.6 - - + -
293C ARG* 3.3 6.4 - - - +
294C CYS 3.2 25.4 + - - +
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Residues in contact with THR 127 (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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125C TYR* 4.2 12.1 + - + -
126C ALA* 1.3 77.4 - - - +
128C ASN* 1.3 61.6 + - - +
129C GLU* 3.1 20.3 + - + +
133C LEU* 2.8 32.5 + - - +
134C MET* 3.3 34.0 + - - +
135C PRO* 3.4 17.0 - - + -
176C LYS* 5.8 0.2 + - - -
286C VAL* 4.5 2.0 - - - +
292C ASP 3.6 7.2 - - - -
293C ARG* 4.0 10.7 - - - +
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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