Contacts of the helix formed by residues 43 - 55 (chain D) in PDB entry 1GQT
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 43 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C THR* 5.5 5.8 + - - -
42D GLY* 1.3 71.9 - - - -
44D GLY* 1.3 63.6 + - - +
46D ASN* 3.8 0.4 - - - +
47D GLN* 3.0 30.0 + - - +
110D ILE* 5.9 0.8 - - - +
141D GLN* 3.9 15.9 - - + -
143D GLU* 3.2 34.7 + - + +
166D ASN* 4.9 0.9 + - - +
168D ALA* 3.8 45.9 - - + +
169D PRO* 4.1 8.3 - - - -
255D ASP* 3.8 22.2 + - - +
1310D RIB 2.5 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 3.6 10.4 - - - +
11D GLY* 3.9 4.9 - - - -
12D SER* 3.4 19.4 + - - -
42D GLY 3.3 0.6 - - - -
43D LYS* 1.3 78.3 - - - +
45D ALA* 1.3 57.8 + - - +
47D GLN* 3.1 2.3 + - - -
48D ALA* 2.8 24.6 + - - +
60D PHE* 3.6 7.6 - - - -
141D GLN* 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D SER 2.8 16.5 + - - +
13D ILE* 3.9 9.9 - - + -
41D GLY 3.7 7.9 - - - +
42D GLY 3.2 0.2 + - - -
44D GLY* 1.3 74.4 - - - +
46D ASN* 1.3 61.0 + - - +
48D ALA* 3.2 2.0 + - - +
49D VAL* 2.8 35.0 + - - +
60D PHE* 3.4 23.1 - - + -
73D VAL* 5.7 0.4 - - + -
77D LEU* 4.4 8.5 - - + -
292D GLN* 3.3 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLY* 3.4 7.1 - - - -
42D GLY 2.7 24.3 + - - +
43D LYS 3.8 0.2 - - - +
45D ALA* 1.3 71.6 - - - +
47D GLN* 1.3 58.5 + - - +
49D VAL* 3.4 1.9 + - - +
50D ALA* 2.9 28.8 + - - +
252D ALA* 3.9 6.3 - - + +
255D ASP* 2.9 37.7 + - + +
291D ALA* 3.6 14.5 - - - +
292D GLN* 3.0 34.4 + - - +
295D VAL* 4.5 6.8 - - + +
1310D RIB 3.1 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 4.8 3.9 - - + +
43D LYS* 3.0 15.5 + - - +
44D GLY 3.6 3.1 - - - +
46D ASN* 1.3 76.1 - - - +
48D ALA* 1.3 63.0 + - - +
50D ALA* 3.4 0.4 + - - -
51D ALA* 3.0 23.9 + - - +
139D LEU* 3.3 31.3 - - + +
141D GLN* 2.8 39.4 + - - +
166D ASN* 2.7 29.6 + - - +
255D ASP* 3.1 44.3 + - - +
258D ASN* 3.8 10.3 - - + +
259D GLY* 3.7 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 4.2 9.1 - - + +
44D GLY 2.8 16.1 + - - +
45D ALA 3.2 4.0 + - - +
47D GLN* 1.3 77.7 - - - +
49D VAL* 1.3 56.1 + - - +
51D ALA* 3.3 2.4 + - - +
52D GLY* 2.8 27.5 + - - -
58D ILE* 3.6 27.2 - - + +
60D PHE* 4.1 20.2 - - + -
82D ILE* 3.7 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ALA 2.8 21.4 + - - +
46D ASN 3.8 3.8 - - - +
48D ALA* 1.3 72.7 - - - +
50D ALA* 1.3 62.1 + - - +
52D GLY 4.5 0.2 - - - +
53D ARG* 2.8 71.8 + - - +
77D LEU* 3.7 17.9 - - + -
80D ASP* 3.9 13.2 - - - +
82D ILE* 4.0 7.0 - - + -
292D GLN* 3.6 29.2 - - + +
295D VAL* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ASN 2.9 17.1 + - - +
47D GLN 3.8 4.3 - - - +
49D VAL* 1.3 77.0 - - - +
51D ALA* 1.3 51.5 + - - +
53D ARG* 4.4 0.3 - - - +
54D SER* 2.5 40.2 + - - -
255D ASP 4.1 0.9 - - - +
256D THR* 3.8 30.7 - - + +
259D GLY* 3.8 11.2 - - - -
260D ALA* 4.3 1.5 - - + +
295D VAL* 3.2 23.0 - - + +
296D PRO 5.1 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU* 3.7 29.4 - - + -
9D VAL* 5.1 1.1 - - + -
47D GLN 3.0 17.7 + - - +
48D ALA* 3.7 4.3 - - - +
50D ALA* 1.3 77.0 - - - +
52D GLY* 1.3 58.1 + - - +
54D SER 3.2 1.7 + - - -
55D GLY 2.9 24.3 + - - -
56D ALA* 2.9 13.8 + - + -
58D ILE* 4.5 6.3 - - + -
139D LEU* 5.9 0.7 - - + -
259D GLY* 3.6 12.9 - - - +
263D THR* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ALA 2.8 20.5 + - - -
51D ALA* 1.3 74.4 - - - +
53D ARG* 1.3 60.9 - - - +
55D GLY* 3.0 7.3 + - - -
56D ALA 4.5 0.2 - - - -
58D ILE* 3.7 18.7 - - - +
80D ASP 3.5 17.3 - - - -
81D ASN* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 2.8 36.6 + - + +
50D ALA 4.4 0.7 - - - +
52D GLY* 1.3 72.6 - - - +
54D SER* 1.3 59.5 + - - +
55D GLY* 3.3 0.9 + - - -
76D GLN* 3.7 11.9 - - - +
80D ASP* 2.6 38.4 + - + +
292D GLN* 2.8 31.7 + - - +
293D PRO* 4.3 7.5 + - - +
295D VAL* 3.0 26.5 + - + +
296D PRO 3.6 13.2 - - - +
297D TRP* 3.5 55.2 - - + +
298D ARG* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ALA 2.5 28.6 + - - -
51D ALA 3.2 0.2 + - - -
53D ARG* 1.3 77.0 - - - +
55D GLY* 1.3 58.6 + - - +
260D ALA* 3.6 12.0 - - - -
263D THR* 3.2 22.4 + - - +
277D PHE* 4.0 12.6 - - - -
296D PRO 4.5 0.8 + - - -
298D ARG* 3.1 37.0 + - - +
301D ILE* 3.7 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ALA* 5.8 2.4 - - - +
51D ALA 2.9 2.4 + - - -
52D GLY 3.0 10.4 + - - -
53D ARG 3.2 1.1 - - - -
54D SER* 1.3 80.1 - - - +
56D ALA* 1.3 69.0 + - - +
57D ASN* 3.8 4.5 + - - +
81D ASN* 4.3 5.5 + - - -
263D THR* 4.0 4.9 - - - -
267D GLU* 4.6 5.6 - - - +
298D ARG* 4.7 7.2 - - - -
----------------------------------------------------------
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