Contacts of the helix formed by residues 315 - 330 (chain B) in PDB entry 2CXQ
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 ASN 315 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.2 1.1 - - - -
81B ARG* 4.1 3.2 - - - +
306B HIS* 3.7 7.5 + - - -
307B PHE* 2.9 35.3 + - - -
310B THR* 2.9 23.2 + - - +
311B PRO 3.5 12.8 - - - +
312B LEU* 3.2 14.8 + - - +
314B LYS* 1.3 74.4 - - - +
316B ALA* 1.3 65.0 + - - +
317B PRO* 3.3 24.8 - - - +
318B VAL* 3.1 17.0 + - + +
319B LEU* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.7 19.9 - - + +
44B LEU* 4.0 16.8 - - + -
53B VAL* 4.3 9.7 - - + +
303B MET* 5.0 0.4 - - - -
306B HIS* 3.0 20.9 + - + +
314B LYS 3.7 2.4 + - - -
315B ASN* 1.3 69.6 - - - +
317B PRO* 1.3 68.9 - - + +
319B LEU* 3.2 4.0 + - - +
320B LEU* 3.0 29.7 + - - +
493B MET* 4.2 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 4.3 6.1 - - - -
306B HIS* 3.8 9.9 - - + -
307B PHE* 3.7 21.5 - - + -
315B ASN* 3.3 17.5 - - - +
316B ALA* 1.3 94.0 - - + +
318B VAL* 1.3 55.1 - - - +
320B LEU* 4.5 3.4 - - + -
321B ALA* 3.0 29.5 + - - +
493B MET* 3.4 36.1 - - + +
496B HIS* 3.6 19.1 - - + +
497B LYS* 3.5 11.1 - - - +
500B VAL* 4.9 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 4.5 9.4 - - + -
77B VAL* 4.7 2.2 - - + -
307B PHE* 3.8 19.3 - - + -
312B LEU* 3.8 37.9 - - + +
315B ASN* 3.1 33.5 + - + +
317B PRO* 1.3 76.8 - - - +
319B LEU* 1.3 59.0 + - - +
321B ALA* 3.2 7.0 + - - +
322B LEU* 2.9 47.5 + - + +
500B VAL* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.9 18.6 - - + -
53B VAL* 6.3 1.6 - - + -
55B TYR* 3.5 42.2 - - + +
65B MET* 3.8 24.0 - - + +
69B VAL* 4.4 9.6 - - + -
312B LEU 3.7 16.2 - - - +
313B GLU* 3.5 23.3 - - - +
314B LYS* 4.2 0.7 - - - -
315B ASN 2.9 17.1 + - - +
316B ALA* 3.8 4.7 - - - +
318B VAL* 1.3 75.2 - - - +
320B LEU* 1.3 61.7 + - + +
322B LEU* 3.3 8.0 + - + +
323B LEU* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.9 23.6 - - + -
55B TYR* 5.5 0.4 - - + -
316B ALA 3.0 19.1 + - - +
317B PRO* 3.9 4.3 - - + +
319B LEU* 1.3 75.3 - - + +
321B ALA* 1.3 61.8 + - - +
323B LEU* 3.5 8.7 + - + +
324B GLY 3.1 17.3 + - - -
405B ASP* 5.0 3.8 - - - +
475B ASN* 3.6 29.3 - - - +
477B ILE* 4.5 11.9 - - + -
493B MET* 3.8 41.5 - - + -
494B TYR* 4.7 11.9 - - + -
497B LYS* 3.7 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO 3.0 19.0 + - - +
318B VAL 3.2 5.1 + - - +
320B LEU* 1.3 78.2 - - - +
322B LEU* 1.3 55.8 + - - +
324B GLY 3.2 0.3 + - - -
325B ILE* 3.0 29.9 + - + +
497B LYS* 3.5 30.2 - - - +
500B VAL* 3.6 22.7 - - + -
501B GLN* 3.0 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B MET* 5.2 2.9 - - + -
68B LEU* 3.2 60.4 - - + +
69B VAL* 3.7 20.0 - - + +
72B ALA* 4.0 4.3 - - + -
318B VAL* 2.9 35.7 + - + +
319B LEU* 3.7 11.9 - - + +
321B ALA* 1.3 73.8 - - + +
323B LEU* 1.3 65.9 + - - +
325B ILE* 3.2 5.5 + - + +
326B TRP* 3.0 23.0 + - - +
504B MET* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.6 34.5 - - + -
58B ASN* 3.8 24.0 - - + +
60B VAL* 3.8 30.5 - - + -
65B MET* 4.1 17.0 - - + -
68B LEU* 4.9 0.9 - - + -
319B LEU* 3.0 24.2 + - + +
320B LEU* 3.8 8.3 - - + +
322B LEU* 1.3 75.5 - - - +
324B GLY* 1.3 62.5 + - - +
326B TRP* 3.3 5.6 + - + +
327B TYR* 3.0 40.4 + - + -
475B ASN* 3.8 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU 3.1 12.5 + - - -
321B ALA 3.2 0.4 + - - -
323B LEU* 1.3 77.4 - - - +
325B ILE* 1.3 55.3 + - - +
327B TYR* 3.2 6.5 + - - +
328B ILE* 2.8 40.8 + - - +
336B HIS* 5.8 5.6 - - - -
497B LYS* 5.2 4.0 - - - -
501B GLN* 3.5 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 5.3 2.9 - - + -
10B PHE* 5.1 2.5 - - + -
13B LEU* 5.0 4.3 - - + -
68B LEU* 4.8 5.4 - - + -
71B LEU* 4.5 22.2 - - + -
321B ALA 3.0 22.1 + - - +
322B LEU* 3.2 8.5 + - - +
324B GLY* 1.3 73.9 - - - +
326B TRP* 1.3 57.6 + - - +
328B ILE* 4.5 1.6 - - - +
329B ASN* 2.7 48.7 + - + +
330B CYS* 3.8 0.5 + - - -
501B GLN* 3.9 13.2 - - + +
504B MET* 4.2 28.5 - - + -
505B TRP* 3.5 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.7 34.5 - - + -
16B TRP* 3.9 23.6 - + - -
17B HIS* 3.6 26.5 - + + -
24B LEU* 4.0 13.0 - - + -
59B LEU 2.8 27.4 + - - -
60B VAL* 3.8 15.4 - - + +
64B VAL* 3.8 18.2 - - + -
68B LEU* 4.1 13.2 - - + +
322B LEU 3.0 12.6 + - - +
323B LEU* 3.3 9.2 - - + +
325B ILE* 1.3 77.0 - - - +
327B TYR* 1.3 82.0 + + - +
330B CYS* 3.1 48.8 + - + +
331B TYR* 3.2 19.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 2.7 36.2 + - + +
59B LEU* 3.0 27.1 + - + -
323B LEU* 3.0 31.0 + - + +
324B GLY* 3.9 5.4 - - - +
326B TRP* 1.3 94.7 - + - +
328B ILE* 1.3 59.3 + - + +
331B TYR* 3.4 28.7 - + + +
332B GLY 3.0 9.5 + - - -
333B CYS* 2.9 27.0 + - + +
401B MET* 4.6 6.3 - - - -
403B PRO* 3.7 38.8 - - + -
473B PRO* 3.1 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS* 4.5 3.6 - - - +
324B GLY* 2.8 30.7 + - - +
325B ILE 4.1 1.1 - - - +
327B TYR* 1.3 75.7 - - + +
329B ASN* 1.3 68.5 + - - +
332B GLY* 3.2 23.2 - - - -
333B CYS* 3.8 19.0 - - + +
335B THR 5.9 0.7 - - - +
374B GLN* 3.6 24.6 - - + +
375B THR 3.5 18.2 - - - +
377B PRO* 3.8 39.3 - - + -
501B GLN* 4.5 4.9 - - - +
505B TRP* 3.8 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.0 7.2 - - - +
10B PHE* 3.8 23.8 - - + -
14B LEU* 3.8 15.4 - - - +
325B ILE* 2.7 34.7 + - + +
328B ILE* 1.3 74.3 - - - +
330B CYS* 1.3 59.2 + - - +
332B GLY* 4.6 0.9 - - - -
373B HIS* 4.0 11.1 + - - +
374B GLN* 3.0 40.6 + - - +
505B TRP* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 4.7 5.4 - - - -
13B LEU* 3.7 33.0 - - - -
14B LEU* 4.2 24.9 - - - +
17B HIS* 3.2 39.3 + - + -
325B ILE 4.8 0.7 - - - -
326B TRP* 3.1 30.6 + - + +
329B ASN* 1.3 84.8 - - - +
331B TYR* 1.3 59.5 + - - +
332B GLY* 3.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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