Contacts of the strand formed by residues 299 - 306 (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 THR 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ASN* 4.3 2.6 + - - +
222B LYS* 5.7 5.8 + - - +
226B ASP 4.5 10.6 + - - -
227B PHE* 3.7 15.1 - - + -
228B ALA* 2.9 32.3 + - - +
297B GLY 4.2 4.5 + - - -
298B GLU* 1.3 76.7 - - - +
300B ILE* 1.3 73.5 + - - +
315B SER* 3.6 21.5 - - - +
316B ALA 3.3 13.7 - - - +
317B THR* 3.6 10.7 + - - -
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.1 22.4 - - + -
227B PHE* 3.7 2.5 - - - -
229B SER* 3.3 12.3 - - - +
231B CYS* 4.1 13.9 - - + -
285B LEU* 4.3 13.0 - - + -
288B LEU* 3.9 15.0 - - + -
289B LEU* 4.4 8.7 - - + -
294B LEU* 3.9 30.1 - - + -
298B GLU* 6.5 0.2 - - + -
299B THR* 1.3 77.2 - - - +
301B GLY* 1.3 70.4 + - - +
302B LEU* 3.7 19.1 - - + +
315B SER* 3.2 7.4 - - - -
316B ALA* 2.8 35.8 + - + +
318B LEU* 4.4 6.7 - - + -
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Residues in contact with GLY 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B PHE* 3.5 21.9 - - - -
229B SER 2.9 10.6 + - - -
230B LEU* 3.0 10.0 - - - +
231B CYS 2.8 25.1 + - - +
300B ILE* 1.3 73.0 - - - +
302B LEU* 1.3 61.6 + - - -
313B PHE* 3.8 15.4 - - - -
314B TYR 3.7 4.3 - - - -
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Residues in contact with LEU 302 (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* 6.0 0.2 - - + -
231B CYS* 3.1 8.3 - - + +
281B LEU* 4.3 19.7 - - + -
282B TYR* 4.8 0.4 - - + -
285B LEU* 4.2 31.4 - - + -
300B ILE* 3.7 29.8 - - + +
301B GLY* 1.3 75.1 - - - +
303B PHE* 1.3 60.2 + - - +
304B SER 4.2 0.2 - - - -
312B GLU 3.6 0.9 - - - +
313B PHE* 3.2 10.7 - - - -
314B TYR* 2.8 83.9 + - + +
316B ALA* 4.1 16.4 - - + -
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Residues in contact with PHE 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B TYR* 4.3 16.6 - + - -
208B SER* 3.6 13.0 - - - -
209B PHE* 3.4 69.3 - + + -
212B SER* 3.7 14.6 - - - -
231B CYS 2.9 7.5 + - - -
232B PHE* 3.4 18.1 - + + -
233B HIS 3.3 24.1 + - - -
281B LEU* 3.8 5.5 - - - +
301B GLY 4.3 0.2 + - - -
302B LEU* 1.3 74.5 - - - +
304B SER* 1.3 74.0 + - - +
305B TYR* 3.7 20.6 - - + -
311B GLY* 3.8 0.7 - - - -
312B GLU 3.3 24.7 - - - -
313B PHE* 4.1 6.1 - - + -
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Residues in contact with SER 304 (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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111B SCY 4.3 3.5 + - - -
112B TYR* 3.6 23.1 + - - -
115B THR* 2.6 38.1 + - - -
233B HIS* 4.8 1.1 - - - -
281B LEU* 3.5 16.9 - - - +
282B TYR* 5.1 0.7 - - - -
302B LEU 4.2 0.4 - - - -
303B PHE* 1.3 77.0 - - - +
305B TYR* 1.3 60.2 + - - +
311B GLY* 3.2 5.2 - - - -
312B GLU 2.9 35.5 + - - -
314B TYR* 4.9 1.8 - - - -
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Residues in contact with TYR 305 (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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111B SCY 3.1 29.8 + - - +
112B TYR* 3.8 4.0 - - - -
184B ASP* 2.9 20.4 + - - -
204B ALA* 3.3 21.1 - - - +
205B TYR* 3.6 39.3 - + + -
208B SER* 3.5 37.9 - - - -
233B HIS* 4.0 13.1 - + + +
303B PHE* 3.7 15.0 - + + -
304B SER* 1.3 76.7 + - - +
306B GLY* 1.3 72.9 + - - +
307B SER* 3.7 20.9 - - - -
309B SER* 3.3 21.6 - - - -
310B VAL 3.5 3.6 - - - -
2402B CAA 3.8 16.8 - - - -
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Residues in contact with GLY 306 (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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109B GLU* 3.5 5.4 - - - -
110B ALA* 3.8 1.8 - - - -
111B SCY 3.3 7.4 - - - -
112B TYR* 3.6 20.8 - - - +
305B TYR* 1.3 78.6 - - - +
307B SER* 1.3 69.0 + - - -
309B SER* 3.1 5.0 - - - -
310B VAL 2.8 29.9 + - - +
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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