Contacts of the helix formed by residues 443 - 455 (chain A) in PDB entry 2GPV
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 443 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASP* 5.0 7.6 + - - +
262A ILE* 4.5 13.2 - - + -
441A GLU* 2.7 48.9 + - + +
442A GLY* 1.3 72.5 - - - -
444A VAL* 1.3 65.6 + - + +
446A MET* 3.1 25.8 + - + +
447A HIS* 3.2 12.5 + - - +
302E GLN* 5.2 9.3 - - + +
305E TRP* 6.3 0.9 - - - +
432E VAL* 6.0 0.9 - - - -
436E TYR* 3.9 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 3.9 33.8 - - + +
265A LEU* 5.2 6.5 - - + -
266A THR* 5.0 2.2 - - - +
438A ILE* 4.7 27.1 - - + +
439A LYS* 5.9 7.0 - - + -
442A GLY* 3.2 1.3 - - - -
443A LYS* 1.3 76.8 - - + +
445A PRO* 1.3 73.6 - - + +
447A HIS* 3.3 13.7 + - - +
448A LYS* 3.4 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLY* 3.7 17.3 - - - +
444A VAL* 1.3 98.3 - - + +
446A MET* 1.3 65.8 + - + +
448A LYS* 3.4 10.2 + - + +
449A LEU* 3.0 37.9 + - + +
504E OHT 6.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLY 4.4 11.2 - - - +
443A LYS* 3.1 20.0 + - + +
445A PRO* 1.3 81.5 - - + +
447A HIS* 1.3 61.7 + - - +
449A LEU* 3.1 12.8 + - + +
450A PHE* 3.0 50.5 + - + -
276E LEU* 4.3 13.0 - - + -
302E GLN* 6.3 0.2 - - + -
305E TRP* 3.4 49.4 - - + +
436E TYR* 3.5 19.7 - - + +
504E OHT 4.3 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.5 17.9 - - + +
258A PRO 4.8 1.2 + - - -
260A SER* 3.0 27.0 + - - -
262A ILE* 3.3 45.6 - - + +
263A LYS* 4.6 2.0 - - - -
443A LYS 3.2 3.9 + - - +
444A VAL 3.5 2.7 - - - +
446A MET* 1.3 78.0 - - - +
448A LYS* 1.3 72.1 + - + +
450A PHE* 3.1 20.4 + - - +
451A LEU* 3.1 22.3 + - + +
298E MET* 3.1 32.7 - - + +
302E GLN* 3.7 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 4.6 0.9 - - + -
266A THR* 3.6 34.6 + - - +
444A VAL* 3.4 27.2 + - + +
445A PRO* 3.4 10.2 + - + +
446A MET 3.4 0.4 - - - -
447A HIS* 1.3 89.1 - - + +
449A LEU* 1.3 58.7 + - + +
451A LEU* 3.7 7.6 + - - +
452A GLU* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A PRO* 3.0 34.1 + - + +
446A MET* 3.1 14.3 + - + +
448A LYS* 1.3 76.8 - - + +
450A PHE* 1.3 67.3 + - + +
452A GLU* 3.4 18.0 + - - +
453A MET* 3.1 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A MET* 3.0 51.0 + - + -
447A HIS* 3.1 10.3 + - - +
449A LEU* 1.3 75.8 - - + +
451A LEU* 1.3 56.6 + - - +
453A MET* 3.1 4.3 + - - +
454A LEU* 2.8 45.9 + - + +
276E LEU* 4.8 11.7 - - + -
280E ILE* 3.4 31.0 - - + -
298E MET* 3.9 22.9 - - + -
301E LEU* 4.3 8.7 - - + -
302E GLN* 3.4 45.5 - - + -
305E TRP* 4.7 13.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.1 31.0 - - + -
258A PRO* 3.5 32.1 - - + -
447A HIS* 3.1 20.8 + - + +
448A LYS* 3.9 7.0 - - - +
450A PHE* 1.3 78.9 - - - +
452A GLU* 1.3 64.3 + - - +
454A LEU* 4.5 3.6 - - - -
455A GLU* 3.0 54.4 + - + +
294E LEU* 4.3 12.1 - - + -
298E MET* 3.9 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LYS* 3.1 21.8 + - - +
449A LEU* 3.5 24.1 - - - +
450A PHE 3.1 0.2 - - - -
451A LEU* 1.3 78.1 - - - +
453A MET* 1.3 66.3 + - - +
455A GLU* 3.7 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 3.1 30.7 + - + +
450A PHE 3.1 3.6 + - - +
452A GLU* 1.3 82.8 - - - +
454A LEU* 1.3 62.8 + - - +
455A GLU* 3.3 3.3 + - - -
276E LEU* 4.8 0.9 - - + -
277E VAL* 3.8 45.3 - - + +
280E ILE* 3.0 57.0 - - + -
281E GLY* 5.4 1.8 - - - +
284E LYS* 3.4 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 2.8 23.7 + - + +
451A LEU* 4.2 3.4 - - - +
453A MET* 1.3 72.8 - - - +
455A GLU* 1.3 58.0 + - - +
280E ILE* 4.0 19.1 - - + +
284E LYS* 3.8 36.2 - - + +
289E PHE* 4.2 10.1 - - + -
294E LEU* 3.9 22.6 - - + +
297E GLN* 3.6 36.7 - - + +
298E MET* 4.0 19.3 - - + +
301E LEU* 3.8 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 4.6 17.3 - - - +
451A LEU* 3.0 40.9 + - + +
452A GLU* 4.0 11.0 - - - +
453A MET 3.2 3.0 - - - -
454A LEU* 1.3 80.0 - - - +
284E LYS* 6.1 0.4 - - - -
294E LEU* 4.1 24.6 - - + +
----------------------------------------------------------
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