Contacts of the strand formed by residues 310 - 318 (chain B) in PDB entry 1XPM
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 VAL 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.9 13.5 - - + -
102A ALA 4.4 4.0 - - - +
103A ARG* 4.6 0.2 - - - -
104A CYS* 3.6 25.8 - - + +
109B GLU* 3.8 12.6 - - + -
112B TYR* 3.6 40.7 - - + +
177B ALA* 4.7 0.4 - - + -
178B TYR 3.4 4.5 - - - +
179B THR* 3.7 21.5 - - + +
208B SER* 4.0 3.4 - - - -
304B SER 4.0 0.2 - - - +
305B TYR* 3.5 2.4 - - - -
306B GLY 2.8 32.2 + - - +
309B SER* 1.3 80.1 - - - +
311B GLY* 1.3 67.5 + - - +
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Residues in contact with GLY 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TYR* 4.6 0.9 - - - -
177B ALA* 3.1 5.9 - - - +
178B TYR 2.8 33.1 + - - -
208B SER* 3.2 20.2 + - - -
212B SER* 3.7 6.7 - - - -
303B PHE* 3.8 3.8 - - - -
304B SER 3.2 9.2 - - - -
310B VAL* 1.3 77.0 - - - +
312B GLU* 1.3 62.2 + - - +
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Residues in contact with GLU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 2.8 38.6 + - - +
112B TYR* 2.7 40.0 + - + -
115B THR* 3.5 23.6 - - + +
119B GLN* 3.6 3.8 - - - +
175B ALA* 3.4 10.9 - - - +
176B VAL 3.3 19.7 - - - +
177B ALA* 3.8 2.6 - - - +
212B SER* 4.3 1.1 - - - -
302B LEU 3.6 0.9 - - - +
303B PHE* 3.3 9.5 - - - -
304B SER* 2.9 34.4 + - - +
311B GLY* 1.3 75.5 - - - +
313B PHE* 1.3 68.8 + - - +
314B TYR* 4.1 5.6 - - + -
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA* 3.4 1.2 - - - -
176B VAL* 3.0 34.0 + - - +
209B PHE* 4.2 20.6 - + - -
212B SER* 4.2 23.7 - - - +
213B TRP* 3.5 42.0 - + + -
216B TYR* 3.6 25.6 - + + -
227B PHE* 3.9 17.5 - + - -
230B LEU* 4.4 11.9 - - + -
301B GLY* 3.8 19.7 - - - -
302B LEU 3.2 14.8 - - - -
303B PHE* 4.1 12.8 - + + -
312B GLU* 1.3 74.1 - - - +
314B TYR* 1.3 72.4 + - - +
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B THR* 3.6 22.9 - - + -
118B ILE* 3.5 6.1 - - + +
119B GLN* 3.3 24.2 - - - +
171B LEU* 3.8 17.3 - - + -
172B ASN 5.5 1.1 - - - +
174B ASP* 3.9 7.6 - - - +
175B ALA* 3.7 21.1 - - + +
216B TYR* 4.3 2.0 - - - -
281B LEU* 4.5 4.2 - - + +
282B TYR* 2.7 35.0 + - - -
301B GLY* 3.7 2.1 - - - -
302B LEU* 2.8 68.9 + - + +
304B SER* 4.9 0.7 - - - -
312B GLU* 4.1 14.8 - - + -
313B PHE* 1.3 86.0 - - - +
315B SER* 1.3 72.4 + - - +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 4.2 0.3 - - - -
172B ASN* 3.0 36.4 + - - +
174B ASP* 2.6 32.8 + - - +
216B TYR* 3.5 11.3 + - - -
222B LYS* 5.5 0.7 - - - -
227B PHE* 3.8 6.1 - - - -
299B THR* 3.6 13.6 - - - +
300B ILE 3.2 11.7 - - - -
302B LEU* 4.4 0.2 - - - -
314B TYR* 1.3 87.3 - - - +
316B ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 4.0 23.7 - - + +
170B ALA 3.1 14.8 - - - +
171B LEU* 4.2 14.8 - - + -
172B ASN* 3.6 2.9 - - - +
299B THR* 3.3 3.3 - - - +
300B ILE* 2.8 32.8 + - + +
302B LEU* 4.1 15.9 - - + -
314B TYR* 5.0 0.2 - - + -
315B SER* 1.3 77.3 - - - +
317B THR* 1.3 63.1 + - - +
318B LEU 4.3 0.2 + - - -
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 3.5 4.6 - - - -
170B ALA* 2.9 41.4 + - - +
172B ASN* 3.1 23.7 + - - -
297B GLY* 3.4 25.4 - - - +
298B GLU 3.4 12.1 - - - +
299B THR* 3.6 9.4 + - - +
316B ALA* 1.3 73.9 - - - +
318B LEU* 1.3 72.5 + - - +
319B VAL* 3.5 0.5 + - - +
127D THR* 5.1 13.9 - - + +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ILE 3.7 4.9 - - - +
169B LEU* 3.7 13.1 - - + +
289B LEU* 3.4 32.8 - - + -
294B LEU* 3.1 45.1 - - + -
295B GLN 3.5 22.4 - - - +
296B ALA* 4.0 4.5 - - - -
297B GLY* 2.9 21.5 + - - -
298B GLU* 3.0 16.5 + - + +
300B ILE* 4.4 6.1 - - + -
317B THR* 1.3 78.1 - - - +
319B VAL* 1.3 59.8 + - - +
320B GLU 4.0 0.5 + - - -
322B TYR* 3.8 23.3 - - + +
126D ALA 4.8 1.7 - - - +
127D THR* 5.9 0.7 - - - +
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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