Contacts of the helix formed by residues 375 - 394 (chain A) in PDB entry 1XI1
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 GLU 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS* 4.6 21.9 - - + +
374A SER* 1.3 78.4 - - - +
376A GLY* 1.3 81.1 + - - +
377A ALA 3.2 3.3 + - - -
378A ILE* 3.6 12.5 + - - +
379A LYS* 3.8 7.6 - - - -
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASP 3.2 22.0 - - - -
138A LYS* 4.0 20.6 - - - +
375A GLU* 1.3 77.2 - - - +
377A ALA* 1.3 64.0 + - - -
379A LYS* 3.2 9.1 + - - +
380A GLN* 3.0 26.3 + - - +
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 3.6 45.0 + - + +
138A LYS* 5.0 0.2 - - - +
179A ILE* 3.9 28.9 - - + -
375A GLU 3.2 2.6 + - - +
376A GLY* 1.3 69.6 - - - -
378A ILE* 1.3 66.5 + - + +
380A GLN* 3.0 15.1 + - - +
381A LEU* 3.0 18.9 + - - +
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Residues in contact with ILE 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 4.3 13.2 - - + -
183A GLN* 3.6 42.6 - - + +
367A TRP* 5.4 2.4 - - + -
370A ILE* 3.8 14.3 - - + +
374A SER* 3.2 27.6 - - - +
375A GLU 3.6 5.9 + - - +
376A GLY 3.6 0.2 - - - -
377A ALA* 1.3 81.8 - - + +
379A LYS* 1.3 56.9 + - - +
381A LEU* 3.6 6.5 + - + +
382A ALA* 3.1 25.5 + - - +
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LYS* 3.6 37.4 - - + +
374A SER* 3.9 15.6 - - - +
375A GLU* 3.7 21.7 + - - +
376A GLY 3.2 11.6 + - - +
377A ALA 3.1 0.8 + - - -
378A ILE* 1.3 77.4 - - - +
380A GLN* 1.3 73.7 + - - +
382A ALA* 3.4 6.7 + - - +
383A LYS* 3.1 38.3 + - + +
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Residues in contact with GLN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE* 5.6 13.0 - - + -
132A LYS* 4.6 4.2 - - - +
136A ASP* 3.3 47.0 + - + +
137A PHE* 3.8 20.4 - - + -
376A GLY* 3.0 16.5 + - - +
377A ALA 3.0 7.2 + - - +
379A LYS* 1.3 84.5 - - - +
381A LEU* 1.3 61.8 + - - +
383A LYS* 3.0 37.5 + - - +
384A LEU* 3.0 28.2 + - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.5 0.2 - - + -
137A PHE* 4.4 18.2 - - + -
179A ILE* 3.9 28.3 - - + -
180A GLN* 3.6 48.2 - - + +
183A GLN* 4.3 13.2 - - + -
185A LEU* 3.9 13.4 - - + +
367A TRP* 4.9 4.7 - - + -
377A ALA 3.0 18.7 + - - +
378A ILE* 3.8 8.5 - - + +
380A GLN* 1.3 76.5 - - - +
382A ALA* 1.3 64.5 + - - +
384A LEU* 3.1 13.9 + - + +
385A MET* 2.9 28.9 + - - +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A TRP* 3.7 40.1 - - + +
370A ILE* 4.2 3.1 - - + -
371A LYS* 3.7 20.2 - - - +
378A ILE 3.1 17.2 + - - +
379A LYS 3.5 6.3 - - - +
380A GLN 3.3 0.2 - - - -
381A LEU* 1.3 77.5 - - - +
383A LYS* 1.3 62.2 + - - +
385A MET* 3.2 4.7 + - - +
386A LEU* 3.1 27.8 + - - +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LYS* 3.4 34.1 - - + +
379A LYS* 3.1 24.0 + - + +
380A GLN* 3.0 43.4 + - - +
381A LEU 3.2 0.2 - - - -
382A ALA* 1.3 77.6 - - - +
384A LEU* 1.3 56.6 + - - +
386A LEU* 3.2 8.3 + - - -
387A ASN* 2.8 47.9 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS 3.5 24.0 - - - +
126A LEU* 4.8 2.9 - - + -
127A PRO* 4.1 25.1 - - + -
128A PHE* 4.6 14.4 - - + -
137A PHE* 6.0 0.9 - - + -
180A GLN* 4.0 12.3 - - - +
185A LEU* 5.8 2.0 - - + -
190A ALA* 3.9 16.6 - - + -
194A SER* 4.3 0.2 - - - -
380A GLN 3.0 13.9 + - - +
381A LEU* 3.4 19.3 - - + +
383A LYS* 1.3 76.4 - - - +
385A MET* 1.3 60.0 + - + +
387A ASN* 4.5 4.5 - - + +
388A SER* 2.7 54.1 + - - +
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Residues in contact with MET 385 (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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185A LEU* 4.0 31.0 - - + -
190A ALA 5.3 0.4 - - - +
193A ASP* 3.3 30.1 - - - +
194A SER* 2.9 32.7 + - - +
197A GLY* 4.2 7.2 - - - -
363A PHE* 3.4 24.3 - - + -
367A TRP* 3.8 53.4 - - + +
381A LEU 2.9 19.0 + - - +
382A ALA 3.4 8.1 - - - +
384A LEU* 1.3 78.8 - - - +
386A LEU* 1.3 59.6 + - - +
387A ASN 3.6 0.2 + - - -
389A LEU 3.9 3.5 + - - -
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PRO* 3.3 28.3 - - + +
258A MET* 5.5 2.4 - - - +
363A PHE* 4.4 7.3 - - + -
364A ILE* 4.0 28.5 - - + -
367A TRP* 3.8 33.7 - - + +
368A THR* 3.8 28.0 - - - +
371A LYS* 4.6 17.7 - - + +
382A ALA 3.1 18.4 + - - +
383A LYS* 3.7 7.9 - - - +
385A MET* 1.3 79.3 - - - +
387A ASN* 1.3 64.0 + - - +
389A LEU* 4.3 8.1 + - - +
390A TYR* 5.2 1.6 + - - +
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Residues in contact with ASN 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 5.5 3.8 + - - -
254A TYR* 6.1 0.5 - - - +
255A PRO* 4.4 14.3 - - - +
383A LYS* 2.8 41.7 + - - +
384A LEU* 4.3 4.4 - - + +
386A LEU* 1.3 79.1 - - - +
388A SER* 1.3 62.2 + - - +
389A LEU 3.4 0.8 + - - -
390A TYR* 4.5 11.0 + - - +
391A GLY 5.0 2.8 + - - -
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ALA* 3.7 17.5 - - - +
191A GLY* 3.9 20.6 - - - +
194A SER* 3.4 11.2 - - - -
384A LEU* 2.7 41.2 + - - +
386A LEU 3.5 0.2 - - - -
387A ASN* 1.3 79.1 - - - +
389A LEU* 1.3 65.1 + - - +
390A TYR 3.5 0.4 - - - -
391A GLY* 3.7 9.6 + - - +
392A LYS 3.9 4.5 + - - -
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Residues in contact with LEU 389 (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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194A SER* 3.7 14.4 + - - +
195A LEU* 3.7 44.6 - - + +
198A PHE* 4.1 10.8 - - + -
258A MET* 3.8 12.6 - - + -
360A PHE* 3.8 30.5 - - + -
363A PHE* 3.8 26.5 - - + -
385A MET 3.9 8.2 + - - +
386A LEU 4.7 4.3 - - - +
387A ASN 3.4 1.6 - - - -
388A SER* 1.3 76.0 - - - +
390A TYR* 1.3 69.5 + - - +
392A LYS* 3.0 20.3 + - + +
393A PHE* 3.6 11.2 - - + -
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Residues in contact with TYR 390 (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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226A TYR* 3.0 23.7 + - - -
228A GLY* 5.6 0.9 - - - -
254A TYR* 3.7 41.2 + + + -
258A MET* 3.9 27.1 - - - +
386A LEU 5.2 1.0 + - - +
387A ASN 4.5 9.7 + - - +
388A SER 3.5 0.6 - - - -
389A LEU* 1.3 77.0 - - - +
391A GLY* 1.3 78.2 + - - +
392A LYS 3.0 1.4 + - - -
393A PHE* 3.0 18.5 + - - +
394A ALA* 3.5 23.9 + - + +
430A GLY* 4.6 3.1 - - - -
433A ILE* 4.0 21.5 - - + -
434A THR* 3.4 28.1 - - + +
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Residues in contact with GLY 391 (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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387A ASN 5.0 1.0 + - - -
388A SER* 3.7 9.3 + - - +
389A LEU 3.1 1.4 + - - -
390A TYR* 1.3 95.5 - - - +
392A LYS* 1.3 60.2 + - - +
393A PHE 3.3 0.7 + - - -
394A ALA* 3.5 20.3 + - - +
395A SER* 3.6 6.9 + - - -
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR* 4.5 2.1 + - - +
191A GLY* 3.3 23.6 - - - +
192A SER* 3.0 44.3 + - - +
195A LEU* 4.1 37.6 - - + +
388A SER 3.9 2.3 + - - +
389A LEU 3.0 13.8 + - - +
391A GLY* 1.3 76.0 - - - +
393A PHE* 1.3 60.5 + - + +
395A SER* 3.7 18.8 + - - +
422A LYS* 5.3 8.9 - - - +
425A VAL* 3.3 26.0 - - + +
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Residues in contact with PHE 393 (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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195A LEU* 4.4 13.9 - - + -
198A PHE* 4.6 2.9 - + - -
211A PHE* 3.9 32.1 - + - -
223A ARG* 5.3 0.5 + - - -
258A MET* 4.7 1.1 - - + -
360A PHE* 4.0 24.7 - + - -
389A LEU* 3.6 36.8 - - + -
390A TYR* 3.0 10.8 + - - +
392A LYS* 1.3 75.8 - - - +
394A ALA* 1.3 60.5 + - - +
395A SER* 3.1 11.2 + - - +
425A VAL* 3.9 26.3 + - + +
426A TYR* 3.8 17.4 + - + +
427A THR* 3.8 14.9 + - - -
429A MET* 3.5 23.6 - - + -
430A GLY* 3.8 20.2 - - - +
433A ILE* 4.8 2.9 - - + -
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Residues in contact with ALA 394 (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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223A ARG* 4.2 11.7 + - - +
226A TYR* 3.6 35.3 + - + +
390A TYR* 3.5 29.7 + - + +
391A GLY* 3.5 9.9 + - - +
393A PHE* 1.3 75.5 - - - +
395A SER* 1.3 60.8 + - - +
396A ASN* 4.8 3.5 - - - +
430A GLY* 4.0 7.0 - - - -
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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
------------------------------------------------------------
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