Contacts of the helix formed by residues 312 - 324 (chain D) in PDB entry 3G1Q
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 312 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D HIS* 2.8 40.3 + - - +
307D LEU* 4.7 4.3 - - - -
309D HIS* 2.9 18.8 + - - +
311D ALA* 1.3 85.8 - - - +
313D VAL* 1.4 57.0 + - - +
314D LYS* 3.1 3.8 - - - -
315D HIS* 2.8 44.4 + - + -
316D LEU* 2.9 10.6 + - - +
399D ARG* 5.6 2.9 - - - -
400D TRP* 3.7 34.0 + - + +
452D VAL* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU 5.3 0.7 - - - -
309D HIS 3.8 2.7 + - - +
310D PRO* 3.2 25.9 + - + +
311D ALA 3.6 1.2 - - - -
312D ASN* 1.4 75.6 - - - +
314D LYS* 1.3 68.8 + - + +
316D LEU* 3.3 15.8 + - + +
317D GLU* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D ALA 5.3 0.2 + - - -
312D ASN* 3.0 1.9 + - - -
313D VAL* 1.3 84.8 - - + +
315D HIS* 1.3 68.4 + - + +
317D GLU* 3.2 16.0 + - + +
318D ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 3.9 6.1 - - + -
311D ALA 5.3 1.1 - - - -
312D ASN* 2.8 38.5 + - + +
314D LYS* 1.3 76.8 - - + +
316D LEU* 1.3 57.4 + - - +
318D ALA* 3.3 1.0 + - - +
319D LEU* 2.9 27.0 + - - +
341D PHE* 3.2 33.6 - - + -
400D TRP* 4.0 18.0 + + + -
401D ASP* 3.9 8.6 + - - +
402D PRO* 3.5 29.4 - - + +
403D GLU* 3.9 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 3.5 31.0 - - + +
308D MET* 5.2 3.4 - - - -
312D ASN 2.9 8.2 + - - +
313D VAL* 3.3 17.0 + - + +
315D HIS* 1.3 75.7 - - - +
317D GLU* 1.3 57.9 + - - +
319D LEU* 3.5 8.2 + - + -
320D ARG* 2.9 66.6 + - + +
440D PHE* 3.6 40.2 - - + -
444D ASP* 4.9 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D VAL* 2.9 19.3 + - + +
314D LYS* 3.2 19.2 + - + +
316D LEU* 1.3 76.5 - - - +
318D ALA* 1.3 53.7 + - - +
320D ARG* 3.3 6.4 + - - +
321D LYS* 2.8 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LYS 2.9 15.6 + - - +
315D HIS* 3.3 5.6 + - - +
317D GLU* 1.3 74.0 - - - +
319D LEU* 1.3 63.8 + - - +
321D LYS* 3.2 13.1 + - + +
322D GLU* 3.1 23.4 + - - +
341D PHE* 3.9 28.0 - - + +
403D GLU* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 3.7 32.8 - - + -
315D HIS 2.9 16.1 + - - +
316D LEU* 3.8 6.5 - - + +
318D ALA* 1.3 77.8 - - - +
320D ARG* 1.3 58.7 + - - +
322D GLU* 3.2 7.4 + - - +
323D ILE* 2.9 43.3 + - + +
339D MET* 5.1 0.4 - - + -
341D PHE* 3.6 13.1 - - + -
342D ALA* 3.7 36.6 - - + +
345D CYS* 5.2 1.1 - - - -
436D LEU* 4.6 11.0 - - + +
440D PHE* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D LEU* 2.9 52.7 + - + +
317D GLU* 3.7 6.1 - - - +
319D LEU* 1.3 72.1 - - - +
321D LYS* 1.3 67.0 - - - +
323D ILE* 3.9 9.0 - - + -
324D GLU* 2.9 44.5 + - - +
440D PHE* 2.7 36.2 + - + +
443D TYR 2.7 21.8 + - - -
444D ASP* 2.6 30.4 + - - -
476D ARG* 3.3 31.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASN* 6.2 5.5 - - - +
132B GLU* 4.4 29.1 + - - -
317D GLU* 2.8 29.7 + - + +
318D ALA* 3.2 12.8 + - - +
320D ARG* 1.3 72.3 - - - +
322D GLU* 1.3 59.5 + - - +
324D GLU* 4.6 3.1 - - - +
325D GLU* 3.6 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ALA 3.1 12.9 + - - +
319D LEU* 3.6 10.0 - - - +
320D ARG 3.1 0.2 - - - -
321D LYS* 1.3 76.0 - - - +
323D ILE* 1.3 65.0 + - + +
324D GLU 3.5 0.3 + - - -
325D GLU* 3.5 15.9 + - - +
326D PHE* 3.8 10.9 - - - -
338D GLU 3.7 13.9 - - - +
339D MET* 3.3 22.5 - - + +
340D PRO* 3.3 12.3 - - - +
341D PHE* 3.0 29.0 + - + +
342D ALA* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D LEU* 2.9 41.6 + - + +
320D ARG* 3.9 10.1 - - - +
322D GLU* 1.3 74.2 - - + +
324D GLU* 1.3 65.3 + - + +
325D GLU 3.1 6.6 + - - -
326D PHE* 3.3 29.8 + - + +
330D LEU* 5.7 0.2 - - - +
339D MET* 4.2 11.0 - - + -
436D LEU 4.4 0.2 - - - +
437D ALA* 3.3 51.1 - - + +
440D PHE* 4.0 11.9 - - + +
441D ARG* 3.6 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.4 16.1 - - - +
320D ARG* 2.9 36.8 + - - +
321D LYS* 4.7 2.9 - - - +
323D ILE* 1.3 86.0 - - + +
325D GLU* 1.3 62.1 + - - +
326D PHE 3.3 7.3 + - - +
440D PHE 5.2 0.3 - - - +
441D ARG* 4.7 16.9 - - + +
476D ARG* 2.6 33.1 + - - -
----------------------------------------------------------
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