Contacts of the strand formed by residues 310 - 318 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C VAL* 3.9 13.7 - - + -
102C ALA 4.4 4.3 - - - +
103C ARG* 4.6 0.2 - - - -
104C CYS* 3.7 24.9 - - + +
109D GLU* 3.8 12.1 + - + -
112D TYR* 3.6 40.8 - - + +
177D ALA* 4.7 0.7 - - + -
178D TYR 3.4 6.5 - - - +
179D THR* 3.6 22.2 - - + +
208D SER* 4.0 3.4 - - - -
304D SER 4.0 0.2 - - - +
305D TYR* 3.6 2.9 - - - -
306D GLY 2.9 30.7 + - - -
309D SER* 1.3 81.2 - - - +
311D GLY* 1.3 64.2 + - - +
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Residues in contact with GLY 311 (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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112D TYR* 4.5 0.7 - - - -
177D ALA* 3.1 5.5 - - - +
178D TYR 2.7 33.9 + - - -
208D SER* 3.3 19.5 + - - -
212D SER* 3.7 7.4 - - - -
303D PHE* 3.8 4.3 - - - -
304D SER 3.2 10.3 - - - -
310D VAL* 1.3 77.8 - - - +
312D GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 312 (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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103C ARG* 2.8 38.5 + - - +
112D TYR* 2.6 40.7 + - + -
115D THR* 3.6 23.3 - - + +
119D GLN* 3.6 3.6 - - - +
175D ALA* 3.4 11.8 - - - +
176D VAL 3.3 18.8 - - - +
177D ALA* 3.7 2.6 - - - +
212D SER* 4.3 1.3 - - - -
302D LEU 3.6 1.0 - - - +
303D PHE* 3.3 9.0 - - - -
304D SER* 2.9 32.9 + - - +
311D GLY* 1.3 75.9 - - - +
313D PHE* 1.3 68.9 + - - +
314D TYR* 4.1 4.5 + - + -
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Residues in contact with PHE 313 (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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175D ALA* 3.4 1.2 - - - -
176D VAL* 3.0 30.9 + - - +
209D PHE* 4.1 20.4 - + - -
212D SER* 4.2 23.9 - - - +
213D TRP* 3.5 41.3 - + + -
216D TYR* 3.5 36.7 - + + -
227D PHE* 3.9 8.7 - + - -
230D LEU* 4.2 14.6 - - + -
301D GLY* 3.8 19.3 - - - -
302D LEU 3.2 14.4 - - - -
303D PHE* 4.1 13.2 - + + -
312D GLU* 1.3 74.4 - - - +
314D TYR* 1.3 73.7 + - - +
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Residues in contact with TYR 314 (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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115D THR* 3.7 22.2 - - + -
118D ILE* 3.6 6.3 - - + +
119D GLN* 3.4 24.0 - - - +
171D LEU* 4.0 16.4 - - + -
172D ASN 5.5 0.9 - - - +
174D ASP* 3.8 7.4 - - - +
175D ALA* 3.7 21.1 - - + +
216D TYR* 4.2 2.2 - - - -
281D LEU* 4.4 3.5 - - + +
282D TYR* 2.7 34.6 + - - -
301D GLY* 3.7 1.9 - - - -
302D LEU* 2.8 68.5 + - + +
304D SER* 5.0 0.7 - - - -
312D GLU* 4.1 15.0 - - + -
313D PHE* 1.3 85.6 - - - +
315D SER* 1.3 72.4 + - - +
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Residues in contact with SER 315 (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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171D LEU* 4.1 0.7 - - - -
172D ASN* 2.9 37.5 + - - +
174D ASP* 2.5 33.5 + - - +
216D TYR* 3.6 11.2 + - - -
222D LYS* 5.5 0.9 - - - -
227D PHE* 3.8 5.6 - - - -
299D THR* 3.6 14.0 - - - +
300D ILE 3.2 13.0 - - - -
302D LEU* 4.4 0.4 - - - -
314D TYR* 1.3 85.4 - - - +
316D ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 316 (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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169D LEU* 3.7 27.2 - - + +
170D ALA 3.2 14.1 - - - +
171D LEU* 4.3 14.1 - - + -
172D ASN* 3.6 1.8 - - - +
298D GLU 4.2 0.2 - - - +
299D THR* 3.3 2.9 - - - +
300D ILE* 2.9 31.2 + - + +
302D LEU* 4.2 15.3 - - + -
314D TYR* 5.1 0.2 - - + -
315D SER* 1.3 77.7 - - - +
317D THR* 1.3 64.4 + - - +
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Residues in contact with THR 317 (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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169D LEU* 3.5 4.8 - - - -
170D ALA* 2.9 38.9 + - - +
172D ASN* 3.1 25.3 + - - -
297D GLY* 3.5 31.6 - - - +
298D GLU 3.5 4.5 - - - +
299D THR* 3.4 11.4 + - - +
316D ALA* 1.3 72.5 - - - +
318D LEU* 1.3 72.5 + - - +
319D VAL* 3.5 0.5 + - - +
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Residues in contact with LEU 318 (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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168D ILE 3.7 9.6 - - - +
169D LEU* 3.8 14.1 - - + +
289D LEU* 3.6 29.8 - - + -
294D LEU* 3.1 43.7 - - + -
295D GLN 3.5 22.2 - - - +
296D ALA* 4.0 3.8 - - - -
297D GLY* 2.9 22.1 + - - -
298D GLU* 3.0 18.0 + - + +
300D ILE* 4.6 4.0 - - + -
317D THR* 1.3 77.4 - - - +
319D VAL* 1.3 59.9 + - - +
320D GLU 4.1 0.3 + - - -
322D TYR* 3.9 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