Contacts of the strand formed by residues 120 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A GLN* 1.3 74.5 - - - +
121A LEU* 1.3 61.4 + - - -
122A MET* 3.8 8.6 - - - +
270A VAL* 6.4 0.2 - - - -
271A ASP* 5.4 4.7 - - - -
299A SER* 2.9 3.1 - - - -
300A TYR* 2.6 34.3 + - - +
8B GLU* 4.2 13.9 - - - -
167B GLN* 2.8 21.7 + - - -
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY* 1.3 74.8 - - - +
122A MET* 1.3 67.9 + - - +
123A PHE* 4.1 19.5 - - + -
258A GLY* 3.5 31.1 - - - +
260A GLY* 5.2 2.8 + - - -
271A ASP* 5.3 1.2 + - - +
297A GLN* 3.2 18.2 - - - +
298A VAL 3.1 10.3 - - - +
299A SER* 3.9 9.6 - - - -
5B PHE* 5.2 0.4 - - + -
6B THR 3.0 27.1 - - - +
7B SER* 4.2 8.1 - - - -
8B GLU* 3.8 32.3 + - + +
167B GLN* 4.9 0.9 - - - +
247B ILE* 5.9 0.7 - - + -
252B GLY 4.0 13.9 - - - +
253B GLY* 4.8 0.7 - - - -
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Residues in contact with MET 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY* 3.8 9.4 - - - +
121A LEU* 1.3 88.6 - - - +
123A PHE* 1.3 64.7 + - - +
124A GLY 4.2 0.3 + - - -
258A GLY 5.0 2.5 - - - +
260A GLY* 6.0 0.7 - - - -
270A VAL* 2.8 39.5 - - + +
271A ASP* 3.2 23.3 - - - +
274A ALA* 3.4 10.3 - - + +
275A ALA* 4.1 19.3 - - + -
278A ALA* 5.0 1.2 - - - +
297A GLN* 3.2 7.2 - - - +
298A VAL* 2.6 62.4 + - + +
300A TYR* 3.9 12.3 - - - -
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Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 4.1 13.9 - - + -
122A MET* 1.3 76.2 - - - +
124A GLY* 1.3 62.0 + - - +
250A THR* 5.7 1.7 - - - +
251A TYR* 3.8 15.1 + - - -
255A ALA* 5.9 0.2 - - + -
256A ARG* 3.4 38.7 - - + +
257A HIS* 3.3 34.9 - - - +
258A GLY* 3.8 4.8 - - - +
275A ALA* 5.0 6.2 - - - +
278A ALA* 4.2 3.5 - - - +
295A GLU* 4.0 19.5 - - + -
296A ILE 3.3 13.7 - - - -
297A GLN* 3.2 38.6 - - + -
311A MET* 5.1 4.3 - - + -
360A PHE* 5.6 1.2 - - - -
5B PHE* 4.1 4.5 - + - -
253B GLY 3.5 25.8 - - - -
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Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PHE* 1.3 73.5 - - - +
125A TYR* 1.3 64.5 + - - +
251A TYR* 3.7 5.8 - - - -
275A ALA 4.8 0.2 - - - -
278A ALA* 3.4 32.0 - - - +
279A ARG 3.9 0.4 - - - -
282A ALA* 4.2 2.7 - - - -
295A GLU* 3.3 8.7 - - - +
296A ILE 2.8 32.6 + - - -
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLY* 1.3 74.2 - - - +
126A ALA* 1.3 82.6 + - - +
127A THR* 4.1 12.7 + - - -
135A PRO* 4.1 21.1 - - + -
251A TYR* 2.9 36.0 + + + -
254A MET* 4.1 23.5 + - + +
255A ALA* 3.3 24.0 - - + -
279A ARG* 3.1 26.4 + - - +
282A ALA* 3.7 7.5 - - - +
293A ARG* 3.7 23.8 + - - -
294A CYS 3.6 8.3 - - - -
295A GLU* 3.4 20.6 - - + -
315A PHE* 3.9 26.7 - + - -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 1.3 81.9 - - - +
127A THR* 1.3 64.5 + - - +
133A LEU* 3.7 2.2 - - + +
279A ARG* 3.7 8.7 - - - +
282A ALA* 3.0 39.0 - - + +
283A LYS* 3.3 12.3 - - + +
286A VAL* 4.0 9.2 - - + -
293A ARG* 3.3 5.8 - - - +
294A CYS 3.3 26.4 + - - +
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A TYR* 4.1 12.4 + - + -
126A ALA* 1.3 78.5 - - - +
128A ASN* 1.3 62.0 + - - +
129A GLU* 3.0 19.7 + - + +
133A LEU* 2.8 40.1 + - - +
134A MET 3.3 33.4 - - - +
135A PRO* 3.4 17.5 - - + -
176A LYS* 5.8 0.3 + - - -
286A VAL* 4.5 1.8 - - - +
292A ASP 3.7 7.0 - - - -
293A ARG* 4.1 11.3 - - - +
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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