Contacts of the helix formed by residues 414 - 435 (chain A) in PDB entry 2XAR
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 LYS 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP* 5.2 9.5 + - - -
65A GLU* 5.6 0.2 - - - -
322A TYR* 4.0 11.4 - - - +
412A PRO* 3.3 4.7 + - + +
413A LEU* 1.3 78.0 - - - +
415A ARG* 1.3 60.6 + - - +
416A MET 3.1 2.3 + - - -
417A GLU* 3.2 36.8 + - - +
418A SER 4.2 0.7 + - - -
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Residues in contact with ARG 415 (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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45A ARG* 3.6 24.0 - - - +
411A LYS* 4.0 10.5 - - - +
412A PRO* 3.0 47.2 + - + +
413A LEU 2.9 0.6 + - - -
414A LYS* 1.3 73.0 - - - +
416A MET* 1.3 56.4 + - - +
417A GLU 3.0 2.7 - - - -
418A SER* 2.9 23.7 + - - +
419A TYR* 2.7 67.5 + - + -
500A IHP 2.7 46.9 + - - -
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Residues in contact with MET 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 3.6 25.1 - - + +
318A ALA* 4.0 24.5 - - + +
319A ILE* 3.3 19.6 - - - +
322A TYR* 3.3 47.1 - - + -
357A VAL* 4.3 13.2 - - + -
360A TYR* 3.7 30.3 - - + -
361A LEU* 4.1 13.0 - - + -
412A PRO 4.4 0.2 + - - -
413A LEU* 3.0 21.4 + - + +
415A ARG* 1.3 77.2 - - - +
417A GLU* 1.3 59.3 + - - +
419A TYR* 3.6 7.5 - - - +
420A TYR 3.3 13.2 + - - -
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 4.4 5.2 - - - -
322A TYR* 3.3 22.2 + - + -
323A TYR* 3.5 29.2 + - - +
326A ILE* 5.1 1.4 - - - +
328A GLN* 5.1 5.4 + - - +
414A LYS* 3.2 38.7 + - - +
415A ARG 3.0 0.4 - - - -
416A MET* 1.3 75.1 - - - +
418A SER* 1.3 65.0 + - - +
420A TYR* 3.2 7.0 + - - +
421A LYS* 3.2 36.0 + - - +
224B ARG* 5.6 3.6 + - - -
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Residues in contact with SER 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LYS 4.2 0.6 + - - -
415A ARG* 2.9 34.3 + - - +
417A GLU* 1.3 76.3 - - - +
419A TYR* 1.3 60.6 + - - +
421A LYS* 3.9 9.2 - - - +
422A LEU* 2.9 33.4 + - - +
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Residues in contact with TYR 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 4.8 8.4 + - - +
315A ILE* 3.8 15.4 - - + +
360A TYR* 3.7 31.6 - + - +
361A LEU* 4.2 15.3 - - + -
364A ALA* 4.1 7.7 - - + +
411A LYS* 3.5 19.1 - - - +
415A ARG* 2.7 53.1 + - + +
416A MET* 3.6 11.4 - - - +
417A GLU 3.2 0.2 - - - -
418A SER* 1.3 73.1 + - - +
420A TYR* 1.3 57.5 + - - +
422A LEU* 3.6 13.4 - - + +
423A ASP* 3.0 31.0 + - - +
500A IHP 2.7 43.2 + - - -
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 3.5 15.1 - - + +
316A GLU* 4.4 23.6 + - + +
319A ILE* 3.6 50.5 - - + -
332A ILE* 3.4 38.4 - - + +
416A MET 3.3 1.8 + - - +
417A GLU* 3.2 9.5 + - - +
419A TYR* 1.3 76.9 - - - +
421A LYS* 1.3 75.2 + - + +
423A ASP* 3.4 3.3 + - - +
424A LYS* 2.9 51.1 + - + +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLU* 3.2 26.0 + - - +
418A SER* 3.9 7.2 - - - +
419A TYR 3.4 0.2 - - - -
420A TYR* 1.3 88.0 - - + +
422A LEU* 1.3 58.5 + - - +
424A LYS* 3.5 7.5 + - + +
425A LYS* 3.0 29.7 + - - +
219B SER* 5.7 6.3 - - - +
224B ARG* 6.1 0.8 - - - +
309B LYS* 5.3 11.4 - - - +
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Residues in contact with LEU 422 (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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192A ARG* 3.8 21.8 - - - +
196A HIS* 4.1 21.3 - - - +
199A LEU* 4.9 7.4 - - + -
418A SER 2.9 19.5 + - - +
419A TYR* 3.6 10.1 - - + +
421A LYS* 1.3 76.0 - - - +
423A ASP* 1.3 58.1 + - - +
425A LYS* 3.0 16.2 + - + +
426A ILE* 2.9 41.1 + - + +
500A IHP 4.0 18.6 - - - +
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Residues in contact with ASP 423 (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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187A LYS* 2.6 41.9 + - - +
192A ARG* 2.9 32.1 + - - +
195A MET* 5.8 1.0 - - - +
314A ASP* 5.1 1.7 - - - +
315A ILE* 3.4 24.1 - - + +
316A GLU* 3.8 7.1 - - - +
419A TYR 3.0 18.7 + - - +
420A TYR* 3.8 3.1 - - - +
422A LEU* 1.3 75.2 - - - +
424A LYS* 1.3 63.5 + - - +
426A ILE* 3.1 6.6 + - - +
427A ILE* 3.0 23.6 + - - +
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Residues in contact with LYS 424 (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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184A ASN* 5.7 3.1 - - - +
316A GLU* 5.6 2.0 - - - +
420A TYR* 2.9 44.7 + - + +
421A LYS* 3.6 8.1 - - + +
423A ASP* 1.3 78.1 + - - +
425A LYS* 1.3 51.7 - - - +
427A ILE* 3.3 10.5 - - + +
428A SER* 2.6 40.8 + - - +
302B ASP* 6.0 4.8 - - - +
306B GLU* 5.7 4.3 - - - -
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.0 23.9 - - + +
203A TYR* 3.2 40.5 + - - -
421A LYS 3.0 13.5 + - - +
422A LEU* 3.0 22.2 + - + +
424A LYS* 1.3 74.6 - - - +
426A ILE* 1.3 63.2 + - + +
428A SER* 3.0 15.1 + - - -
429A PHE* 3.1 17.8 + - + +
176B THR* 4.2 17.2 - - - +
309B LYS* 6.2 6.1 - - + -
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Residues in contact with ILE 426 (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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192A ARG* 4.6 12.6 - - - +
195A MET* 3.6 45.9 - - + +
196A HIS* 3.1 36.1 - - + +
199A LEU* 3.4 28.9 - - + -
422A LEU* 2.9 31.4 + - + +
423A ASP* 3.5 10.1 - - - +
425A LYS* 1.3 75.9 - - - +
427A ILE* 1.3 60.3 + - + +
429A PHE* 3.3 5.7 + - - +
430A TYR* 2.9 27.0 + - - +
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Residues in contact with ILE 427 (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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184A ASN* 3.5 45.5 - - + +
186A LEU* 4.3 3.8 - - + -
187A LYS* 3.5 41.7 - - + +
195A MET* 3.7 20.0 - - + -
316A GLU* 4.7 1.6 - - - +
423A ASP* 3.0 20.2 + - - +
424A LYS* 3.3 17.3 - - + +
426A ILE* 1.3 77.1 - - + +
428A SER* 1.3 64.5 + - - +
430A TYR* 4.5 3.6 - - + -
431A ASN* 3.0 43.3 + - - +
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Residues in contact with SER 428 (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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184A ASN* 5.5 1.3 - - - -
424A LYS* 2.6 30.0 + - - +
425A LYS* 3.0 15.1 + - - -
427A ILE* 1.3 77.9 - - - +
429A PHE* 1.3 54.6 + - - +
431A ASN* 3.3 8.4 + - - +
432A ARG* 2.8 31.8 + - - +
306B GLU* 6.0 3.4 - - - -
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Residues in contact with PHE 429 (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 MET 5.5 1.1 - - - -
198A LEU* 3.4 38.6 - - + -
199A LEU* 4.0 23.1 - - + -
202A GLU* 3.6 40.6 - - + -
425A LYS* 3.1 17.9 + - + +
426A ILE* 3.7 3.8 - - - +
428A SER* 1.3 76.4 + - - +
430A TYR* 1.3 59.0 + - + +
432A ARG* 3.5 22.1 - - - +
433A LYS* 3.0 57.4 + - + +
312B LYS* 4.3 11.2 - - - -
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Residues in contact with TYR 430 (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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186A LEU* 3.9 21.1 - - + -
190A VAL* 3.8 31.8 - - + +
194A LYS* 4.7 13.6 + - + -
195A MET* 3.6 48.9 - - + +
198A LEU* 3.7 28.7 - - + -
426A ILE 2.9 17.2 + - - +
427A ILE* 4.0 3.8 - - + +
428A SER 3.3 0.2 - - - -
429A PHE* 1.3 78.7 - - + +
431A ASN* 1.3 63.0 + - - +
433A LYS* 3.5 4.6 + - - +
434A GLN* 2.9 62.3 + - + +
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Residues in contact with ASN 431 (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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183A GLU* 2.8 36.9 + - - +
184A ASN* 3.8 4.6 + - - -
186A LEU* 3.6 27.6 - - - +
427A ILE* 3.0 33.3 + - - +
428A SER* 3.6 6.7 - - - +
430A TYR* 1.3 75.9 - - - +
432A ARG* 1.3 57.3 + - - +
434A GLN* 3.0 8.5 + - - +
435A LYS* 2.9 31.3 + - - +
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Residues in contact with ARG 432 (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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428A SER 2.8 18.2 + - - +
429A PHE* 3.5 24.3 - - + +
431A ASN* 1.3 76.9 - - - +
433A LYS* 1.3 61.6 + - + +
435A LYS* 3.5 16.5 + - - +
436A ALA* 3.8 5.5 + - - +
96B LEU* 3.6 31.1 - - - +
310B LEU* 4.5 20.2 - - - +
312B LYS* 5.4 8.1 - - - +
355B LYS* 6.0 2.4 - - - +
359B GLU* 4.9 7.1 + - - -
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Residues in contact with LYS 433 (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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198A LEU* 4.8 15.5 - - + -
202A GLU* 4.6 8.3 + - - -
429A PHE* 3.0 54.4 + - + +
430A TYR* 3.9 5.2 - - - +
431A ASN 3.3 0.2 - - - -
432A ARG* 1.3 76.8 - - + +
434A GLN* 1.3 69.0 + - - +
436A ALA* 3.4 24.2 + - + +
355B LYS* 4.8 19.2 - - - +
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Residues in contact with GLN 434 (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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186A LEU* 4.1 13.7 - - + +
198A LEU* 4.8 4.6 - - - +
430A TYR* 2.9 63.7 + - + +
431A ASN* 3.0 9.8 + - - +
433A LYS* 1.3 78.3 + - - +
435A LYS* 1.3 62.2 + - - +
436A ALA 3.0 10.2 + - - +
437A GLU* 3.4 20.9 - - - +
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ASN 2.9 15.7 + - - +
432A ARG* 3.7 9.6 - - - +
433A LYS 3.4 0.4 - - - -
434A GLN* 1.3 75.0 - - - +
436A ALA* 1.3 56.1 + - - +
437A GLU* 3.3 21.7 + - - +
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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
------------------------------------------------------------
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