Contacts of the strand formed by residues 293 - 300 (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 ARG 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TYR* 3.7 18.3 + - - +
126A ALA 3.3 15.0 - - - +
127A THR* 4.1 12.6 - - - +
286A VAL* 3.9 3.1 - - - -
291A ALA* 3.4 1.9 - - - -
292A ASP* 1.3 84.6 - - + +
294A CYS* 1.3 64.0 + - - +
314A THR* 3.3 10.4 - - - +
315A PHE* 3.1 69.9 + - + +
317A THR* 3.1 16.6 + - + +
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Residues in contact with CYS 294 (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 4.5 - - - -
126A ALA 3.3 27.3 + - - -
282A ALA* 3.6 20.6 - - - +
285A ILE* 3.8 36.8 - - + -
286A VAL* 4.3 3.2 - - + +
291A ALA* 4.5 4.5 - - + -
293A ARG* 1.3 75.9 - - - +
295A GLU* 1.3 58.7 + - - +
296A ILE* 4.4 8.7 - - - -
312A VAL* 5.3 2.2 - - - -
313A GLU 3.0 14.6 - - - +
314A THR* 3.4 19.7 - - + -
315A PHE* 3.8 1.3 - - - -
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Residues in contact with GLU 295 (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* 4.0 12.8 - - + -
124A GLY 3.3 11.2 - - - +
125A TYR* 3.4 17.4 - - + -
254A MET 4.8 0.2 - - - +
255A ALA* 3.2 10.9 - - + -
256A ARG* 2.6 68.9 + - - +
294A CYS* 1.3 74.2 - - - +
296A ILE* 1.3 61.2 + - - +
311A MET* 3.7 4.5 - - + +
312A VAL* 3.6 1.9 - - - -
313A GLU* 2.7 41.3 + - + +
315A PHE* 3.8 20.7 - - + -
256B ARG* 5.4 0.3 - - - -
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Residues in contact with ILE 296 (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* 3.2 9.5 - - - -
124A GLY 2.8 29.8 + - - +
278A ALA* 4.2 29.6 - - + +
281A VAL* 3.5 30.7 - - + -
282A ALA* 4.5 3.1 - - + -
285A ILE* 4.6 1.3 - - + -
294A CYS* 4.1 11.2 - - - -
295A GLU* 1.3 76.4 - - - +
297A GLN* 1.3 73.3 + - - +
298A VAL* 4.7 9.6 - - + +
310A ILE* 5.1 4.0 - - + -
311A MET* 3.5 3.8 - - - +
312A VAL* 3.4 37.7 - - + -
329A VAL* 4.5 10.5 - - + -
335A LEU* 6.2 1.6 - - + -
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Residues in contact with GLN 297 (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* 3.2 26.8 - - + +
122A MET 3.2 13.0 - - - +
123A PHE* 3.2 39.3 - - + -
296A ILE* 1.3 80.2 - - - +
298A VAL* 1.3 66.5 + - - +
309A SER* 3.7 6.3 + - - +
310A ILE* 3.1 6.1 + - - +
311A MET* 3.0 49.2 + - + +
4B LEU 4.3 5.5 + - - -
5B PHE* 3.7 20.1 - - - +
6B THR* 3.3 18.6 + - - +
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Residues in contact with VAL 298 (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* 3.1 4.3 - - - +
122A MET* 2.6 59.8 + - + +
274A ALA* 4.1 12.1 - - + +
278A ALA* 5.0 4.7 - - + -
296A ILE* 4.7 7.4 - - + -
297A GLN* 1.3 78.0 - - - +
299A SER* 1.3 59.0 + - - +
300A TYR* 3.7 18.4 - - + +
307A PRO* 5.2 1.8 - - + -
309A SER* 3.0 13.5 - - - +
310A ILE* 3.8 19.5 - - + -
335A LEU* 4.0 26.5 - - + -
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Residues in contact with SER 299 (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 2.9 11.7 - - - -
121A LEU* 3.9 4.9 - - - -
297A GLN* 5.3 0.2 - - - -
298A VAL* 1.3 76.6 - - - +
300A TYR* 1.3 69.1 + - - +
307A PRO* 3.7 3.3 - - - +
308A THR* 2.5 46.2 + - - -
309A SER* 2.9 33.3 + - - -
6B THR* 3.2 24.8 + - - -
167B GLN* 3.9 1.6 - - - -
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Residues in contact with TYR 300 (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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116A ALA* 3.8 20.0 - - + -
118A ASP 3.9 6.5 - - - +
119A GLN* 3.1 4.0 - - - +
120A GLY 2.6 24.7 + - - +
122A MET* 3.9 11.7 - - - -
270A VAL* 3.8 24.2 - - + -
274A ALA* 3.4 27.2 - - + +
298A VAL* 3.7 18.6 - - + +
299A SER* 1.3 77.6 - - - +
301A ALA* 1.3 60.0 + - - +
304A VAL 4.8 2.5 - - - -
305A ALA 4.8 0.9 - - - -
306A GLU 5.1 0.2 - - - -
307A PRO* 3.8 22.7 - - + -
308A THR* 3.6 5.6 - - - +
335A LEU* 2.5 43.7 + - - +
337A PRO* 4.1 10.8 - - + -
340A LEU* 3.6 9.8 - - + +
167B GLN* 2.7 25.4 + - - -
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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