Contacts of the strand formed by residues 120 - 127 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C GLU* 4.1 15.0 - - - -
167C GLN* 2.6 24.5 + - - +
119D GLN* 1.3 75.6 - - - +
121D LEU* 1.3 57.9 + - - -
122D MET* 3.9 9.1 - - - +
270D VAL* 6.3 0.4 - - - -
271D ASP* 5.4 4.7 - - - -
299D SER* 2.9 3.1 - - - -
300D TYR 2.6 32.8 + - - -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C THR* 2.8 28.3 - - - +
7C SER* 4.1 8.1 - - - -
8C GLU* 3.5 32.9 + - + -
167C GLN* 4.8 1.3 - - - +
247C ILE* 6.0 0.7 - - + -
252C GLY 4.0 14.6 - - - +
253C GLY* 4.9 0.2 - - - -
120D GLY* 1.3 74.4 - - - +
122D MET* 1.3 68.8 + - - +
123D PHE* 4.1 19.1 - - + -
258D GLY* 3.4 31.4 - - - +
260D GLY 5.2 2.6 + - - -
271D ASP* 5.3 1.2 + - - +
297D GLN* 3.4 14.4 - - - +
298D VAL 3.2 10.1 - - - +
299D SER* 3.9 10.8 - - - -
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Residues in contact with MET 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLY* 3.9 8.1 - - - +
121D LEU* 1.3 91.7 - - - +
123D PHE* 1.3 64.6 + - - +
124D GLY 4.2 0.3 + - - -
257D HIS* 6.4 0.2 - - - -
258D GLY 5.0 2.9 - - - +
260D GLY* 6.0 0.4 - - - -
270D VAL* 2.9 38.8 - - + +
271D ASP* 3.3 23.1 - - - +
274D ALA* 3.5 10.5 - - + -
275D ALA* 4.1 20.4 - - + -
278D ALA* 5.0 0.8 - - - +
296D ILE 3.8 0.2 - - - +
297D GLN* 3.2 7.7 - - - +
298D VAL* 2.7 58.1 + - + +
300D TYR* 4.0 13.7 - - - -
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Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 4.1 5.4 - + - -
253C GLY* 3.6 20.0 - - - -
121D LEU* 4.1 14.1 - - + -
122D MET* 1.3 75.4 - - - +
124D GLY* 1.3 61.2 + - - +
250D THR* 5.8 1.2 - - - +
251D TYR* 3.8 15.2 + - + -
255D ALA* 5.9 0.2 - - + -
256D ARG* 3.3 41.3 - - + +
257D HIS* 3.3 35.8 - - - +
258D GLY* 3.8 3.9 - - - +
275D ALA* 4.9 6.8 - - - +
278D ALA* 4.2 3.7 - - - +
295D GLU* 3.9 20.2 - - + -
296D ILE 3.3 14.1 - - - -
297D GLN* 3.2 40.2 - - + -
311D MET* 5.1 3.8 - - + -
360D PHE* 5.5 1.9 - - - -
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Residues in contact with GLY 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D PHE* 1.3 73.7 - - - +
125D TYR* 1.3 63.6 + - - +
251D TYR* 3.7 4.3 - - - -
275D ALA 4.8 0.2 - - - -
278D ALA* 3.4 33.0 - - - +
279D ARG 3.9 0.7 - - - -
282D ALA* 4.1 4.0 - - - -
295D GLU* 3.3 7.8 - - - +
296D ILE 2.8 32.6 + - - +
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Residues in contact with TYR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLY* 1.3 73.9 - - - +
126D ALA* 1.3 82.1 + - - +
127D THR* 4.1 10.8 + - + -
135D PRO* 4.1 13.9 - - + -
251D TYR* 3.0 34.6 + + + -
254D MET* 4.1 30.1 + - + +
255D ALA* 3.4 25.4 - - + -
279D ARG* 3.0 27.3 + - - +
282D ALA* 3.7 7.4 - - - +
293D ARG* 3.7 25.8 + - - +
294D CYS 3.5 10.1 - - - -
295D GLU* 3.5 20.4 - - + -
315D PHE* 3.8 26.7 - + - -
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D TYR* 1.3 84.1 - - - +
127D THR* 1.3 64.3 + - - +
133D LEU* 3.7 2.0 - - + +
279D ARG* 3.6 8.5 - - - +
282D ALA* 3.2 35.2 - - + +
283D LYS* 3.3 13.5 - - + +
286D VAL* 3.9 9.9 - - + -
293D ARG* 3.3 6.5 - - - +
294D CYS 3.2 24.8 + - - +
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Residues in contact with THR 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D TYR* 4.1 12.7 + - + -
126D ALA* 1.3 77.1 - - - +
128D ASN* 1.3 61.7 + - - +
129D GLU* 3.1 19.6 + - + +
133D LEU* 2.8 36.2 + - - +
134D MET 3.3 32.8 - - - +
135D PRO* 3.4 17.0 - - + -
286D VAL* 4.4 2.4 - - - +
292D ASP 3.7 7.4 + - - -
293D ARG* 4.0 11.5 - - - +
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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