Contacts of the helix formed by residues 444 - 457 (chain A) in PDB entry 2NQB
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 GLY 444 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A PRO* 1.3 71.2 - - - +
445A THR* 1.3 58.5 + - - +
446A VAL 3.3 2.0 - - - -
447A ALA* 3.6 8.7 - - - +
448A LEU* 2.8 35.9 + - - +
44B LYS* 3.7 26.3 - - - -
45B ARG* 6.3 1.6 - - - -
228J A 3.2 6.8 + - - -
229J A 3.0 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 3.9 22.0 - - + -
442A ARG* 3.0 17.0 + - - +
443A PRO 3.4 1.7 + - - -
444A GLY* 1.3 76.7 - - - +
446A VAL* 1.3 57.5 + - - +
448A LEU* 3.5 8.7 + - - +
449A ARG* 3.2 33.1 + - - +
143I T 3.9 18.2 - - - +
144I G 2.6 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 3.8 16.4 - - + -
445A THR* 1.3 73.9 - - - +
447A ALA* 1.3 60.0 + - - +
449A ARG* 3.2 34.0 + - + +
450A GLU* 2.9 44.7 + - + +
229J A 2.9 26.1 + - + +
230J C 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLY* 3.3 13.4 + - - +
446A VAL* 1.3 75.2 - - - +
448A LEU* 1.3 58.3 + - - +
450A GLU* 3.1 6.2 + - - +
451A ILE* 2.9 33.0 + - - +
39B ARG* 3.5 33.1 - - - +
44B LYS* 3.6 22.4 - - + +
228J A 4.8 2.5 - - - +
229J A 3.0 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLY 2.8 19.1 + - - +
445A THR* 3.6 8.5 - - - +
447A ALA* 1.3 77.8 - - - +
449A ARG* 1.3 60.8 + - - +
451A ILE* 3.4 23.1 + - + +
452A ARG* 3.2 49.8 + - - +
44B LYS* 4.0 19.1 - - + +
1111G ILE* 4.5 15.9 - - + +
1115G LEU* 3.8 20.4 - - + +
1116G LEU* 4.5 1.8 - - + -
1117G PRO* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 3.3 41.8 - - - -
445A THR* 3.2 21.8 + - - +
446A VAL* 3.2 32.4 + - + +
448A LEU* 1.3 76.2 - - - +
450A GLU* 1.3 61.5 + - + +
452A ARG* 3.3 11.3 + - - +
453A ARG* 3.0 30.2 + - + +
143I T 5.5 5.1 - - - -
153J A 3.4 31.7 + - - -
154J T 3.1 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A VAL* 2.9 34.8 + - + +
447A ALA 3.3 7.2 - - - +
449A ARG* 1.3 77.4 - - + +
451A ILE* 1.3 58.8 + - - +
453A ARG* 3.2 6.2 + - - +
454A TYR* 2.8 54.3 + - + -
35B ARG* 4.0 14.7 + - - +
36B ARG* 5.6 1.7 - - - +
39B ARG* 3.1 38.6 + - + +
229J A 4.2 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ALA 2.9 19.1 + - - +
448A LEU* 3.6 27.6 - - + +
449A ARG 3.3 0.2 - - - -
450A GLU* 1.3 75.0 - - - +
452A ARG* 1.3 62.6 + - - +
454A TYR 4.0 0.2 - - - -
455A GLN* 2.9 45.6 + - - +
39B ARG* 3.7 33.4 - - - +
42B GLY* 3.8 17.0 - - - +
43B VAL 3.6 20.2 - - - +
44B LYS* 4.1 7.9 - - + -
1111G ILE* 3.6 27.1 - - + -
1115G LEU* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 3.2 41.7 + - - +
449A ARG* 3.7 10.6 - - - +
451A ILE* 1.3 76.9 - - - +
453A ARG* 1.3 61.8 + - - +
455A GLN* 4.1 3.9 - - - +
456A LYS* 3.3 36.2 + - - +
1111G ILE* 4.8 21.0 - - + +
1116G LEU* 3.7 28.1 - - - +
1117G PRO* 5.6 2.2 - - - +
143I T 5.9 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ARG* 3.0 21.1 + - + +
450A GLU* 3.2 8.3 + - - +
452A ARG* 1.3 78.2 - - - +
454A TYR* 1.3 96.3 + - + +
456A LYS* 3.3 16.6 + - - +
457A SER* 3.3 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A GLU* 2.8 53.9 + - + +
451A ILE 4.4 0.2 - - - +
453A ARG* 1.3 104.3 + - + +
455A GLN* 1.3 63.7 + - - +
456A LYS 3.1 2.2 - - - -
457A SER* 3.4 17.0 + - - +
459A GLU* 4.5 5.8 - - - -
461A LEU* 3.8 22.7 - - + -
36B ARG* 3.4 43.9 + - + +
39B ARG* 3.9 11.2 - - + -
40B ARG* 2.9 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ILE* 2.9 35.1 + - + +
452A ARG* 4.2 3.4 - - - +
454A TYR* 1.3 76.2 - - - +
456A LYS* 1.3 61.7 + - - +
457A SER 4.3 1.1 - - - +
39B ARG 4.0 3.4 - - - +
40B ARG* 3.2 26.5 + - - +
41B GLY 4.2 1.0 - - - -
42B GLY* 3.6 14.8 - - - +
1081G ARG* 3.5 6.2 + - - -
1107G VAL* 3.1 31.4 - - + +
1108G LEU 4.1 5.8 + - - -
1109G PRO* 3.4 16.4 - - + +
1110G ASN* 2.6 48.5 + - - +
1111G ILE* 3.4 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ARG* 3.3 23.9 + - - +
453A ARG* 3.3 8.0 + - - +
454A TYR 3.1 0.6 - - - -
455A GLN* 1.3 81.0 - - - +
457A SER* 1.3 59.2 + - - +
458A THR* 4.5 1.9 - - - +
1081G ARG* 3.1 23.9 + - - +
1109G PRO* 5.2 11.4 - - + -
155J C 4.4 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ARG* 3.3 15.8 + - - +
454A TYR* 3.4 13.3 + - - +
455A GLN 4.3 2.1 - - - +
456A LYS* 1.3 81.5 - - - +
458A THR* 1.3 65.7 + - - +
459A GLU* 2.4 33.4 + - - -
40B ARG* 3.2 17.3 + - - -
1081G ARG* 4.8 0.3 + - - -
1106G GLY* 4.1 6.6 - - - -
1107G VAL 5.0 0.2 + - - -
----------------------------------------------------------
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