Contacts of the helix formed by residues 381 - 391 (chain B) in PDB entry 2XGZ
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 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLU* 6.0 2.2 - - + +
119B ARG* 4.1 8.2 + - - +
379B GLU 3.6 15.3 - - - +
380B ASP* 1.3 75.2 + - - +
382B PHE* 1.3 65.8 + - - +
383B ILE 3.2 2.7 - - - -
384B ALA* 3.1 19.0 + - - +
385B ASP* 3.6 7.7 + - - +
407B ALA* 3.4 31.4 - - + +
408B LYS* 4.4 6.5 - - - -
411B GLN* 3.9 28.3 + - + +
414B ARG* 5.5 2.5 - - - +
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Residues in contact with PHE 382 (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 LEU* 3.6 46.7 - - + -
118B SER* 3.3 24.5 - - - -
119B ARG* 3.5 16.3 - - - +
129B LEU* 3.6 26.7 - - + -
133B LEU* 3.9 10.8 - - + -
346B VAL* 5.2 3.8 - - + -
352B LEU* 3.7 23.6 - - + -
380B ASP* 2.8 19.6 + - - +
381B THR* 1.3 76.7 - - - +
383B ILE* 1.3 67.6 + - + +
385B ASP* 3.1 6.5 + - - +
386B LEU* 2.8 43.1 + - + -
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Residues in contact with ILE 383 (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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346B VAL* 4.7 16.2 - - + +
371B VAL* 3.8 16.2 - - + +
372B SER 4.0 9.6 - - - +
373B HIS* 3.9 28.5 - - - +
377B GLU* 4.6 3.8 - - - +
382B PHE* 1.3 86.8 - - + +
384B ALA* 1.3 59.3 + - - +
386B LEU* 3.7 11.7 - - + +
387B VAL* 2.9 31.2 + - - +
395B ILE* 3.8 8.5 - - + +
397B THR* 3.6 26.7 - - - +
408B LYS* 3.7 24.5 - - + -
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Residues in contact with ALA 384 (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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381B THR 3.1 12.0 + - - +
383B ILE* 1.3 80.0 - - - +
385B ASP* 1.3 62.4 + - - +
387B VAL* 3.3 21.2 - - - +
388B VAL* 3.4 12.3 + - - +
395B ILE* 4.5 3.4 - - - -
408B LYS* 3.5 32.7 - - + +
411B GLN* 3.7 17.5 - - + -
412B LEU* 3.7 14.5 - - + +
415B ILE* 4.2 3.1 - - - -
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 5.5 0.3 + - - -
128B PRO* 5.2 0.2 - - - +
129B LEU* 3.4 35.8 + - + +
130B TYR* 3.0 46.6 + - - +
133B LEU* 3.6 5.8 - - + +
381B THR* 3.6 8.7 + - - +
382B PHE 3.1 8.1 + - - +
384B ALA* 1.3 78.2 - - - +
386B LEU* 1.3 57.2 + - - +
388B VAL 3.4 0.5 + - - -
389B GLY 2.9 24.6 + - - -
411B GLN* 3.0 31.7 + - - +
415B ILE* 4.0 3.6 - - - -
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.5 18.1 - - + +
344B LEU* 4.1 15.7 - - + -
346B VAL* 3.4 32.3 - - + -
352B LEU* 3.9 25.1 - - + -
355B SER* 5.3 0.9 - - - -
356B ILE* 4.6 7.2 - - + -
371B VAL* 4.4 10.8 - - + -
382B PHE* 2.8 29.0 + - + +
383B ILE* 3.7 9.0 - - + +
384B ALA 3.3 0.2 - - - -
385B ASP* 1.3 70.7 - - - +
387B VAL* 1.3 61.6 + - - +
389B GLY* 3.2 0.5 + - - -
390B LEU* 2.8 52.7 + - + +
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Residues in contact with VAL 387 (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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145B VAL 4.7 1.6 - - - +
147B PRO* 3.6 34.3 - - + +
371B VAL* 3.7 21.7 - - + +
383B ILE 2.9 16.7 + - - +
384B ALA 3.3 12.8 - - - +
386B LEU* 1.3 75.5 - - - +
388B VAL* 1.3 59.9 + - - +
390B LEU 3.6 0.6 + - - +
391B ARG* 3.1 20.8 + - - -
392B THR* 3.3 34.2 + - - +
393B GLY 4.7 1.1 + - - +
394B GLN 3.4 15.9 - - - +
395B ILE* 3.9 12.1 - - + -
412B LEU* 4.0 5.4 - - + -
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Residues in contact with VAL 388 (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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130B TYR* 3.9 29.2 - - + -
139B SER* 4.8 0.7 + - - -
144B TYR* 4.2 20.9 - - + -
145B VAL 4.1 15.8 + - - +
146B LEU* 4.1 15.9 - - + -
147B PRO* 4.3 3.8 - - + -
384B ALA 3.4 13.3 + - - +
385B ASP 3.8 6.3 - - - +
386B LEU 3.2 0.4 - - - -
387B VAL* 1.3 77.5 - - + +
389B GLY* 1.3 65.9 + - - +
391B ARG* 3.1 16.1 + - - +
412B LEU* 3.6 21.8 - - + -
415B ILE* 4.1 14.8 - - + -
419B LEU* 4.5 5.4 - - + -
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Residues in contact with GLY 389 (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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130B TYR 3.6 21.9 + - - -
133B LEU* 4.0 7.0 - - - -
134B ALA* 3.3 11.5 - - - -
137B SER* 2.9 11.6 + - - -
139B SER* 2.6 28.8 + - - -
144B TYR* 5.8 0.2 - - - -
385B ASP 2.9 17.6 + - - -
386B LEU 3.6 2.9 - - - -
388B VAL* 1.3 72.9 - - - +
390B LEU* 1.3 55.5 + - - +
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B SER* 3.7 25.6 - - - -
139B SER* 4.4 4.9 - - - -
344B LEU* 4.4 8.5 - - + -
355B SER 5.1 1.8 - - - +
356B ILE* 4.4 16.2 - - + +
359B ALA* 3.9 31.9 - - + -
360B GLN* 5.7 1.8 - - + -
363B PHE* 3.4 23.4 - - + -
371B VAL* 4.4 11.9 - - + -
386B LEU* 2.8 52.1 + - + +
389B GLY* 1.3 70.4 - - - +
391B ARG* 1.3 69.7 + - - +
392B THR* 3.3 16.1 + - + -
434B ASP* 4.5 0.9 - - - +
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B SER* 4.1 10.5 - - - +
140B LYS* 3.0 52.5 + - - +
143B PRO* 2.9 39.0 + - - +
144B TYR* 5.2 0.2 - - - -
145B VAL* 3.5 35.6 - - + +
387B VAL 3.1 3.8 + - - -
388B VAL 3.1 15.7 + - - +
389B GLY 3.3 0.2 - - - -
390B LEU* 1.3 78.6 - - - +
392B THR* 1.3 58.8 + - - +
393B GLY 3.5 2.2 - - - -
433B GLY 3.0 16.6 + - - -
434B ASP* 2.8 52.7 + - + -
435B LYS 4.0 0.4 - - - -
436B LEU 2.6 31.9 + - - +
437B LEU* 5.3 0.2 - - - +
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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