Contacts of the strand formed by residues 42 - 53 (chain B) in PDB entry 6QPA
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 PHE 42 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B CSS 4.9 3.4 - - - -
36B THR* 3.4 36.8 - - + +
37B ALA* 3.7 30.5 - - + -
39B HIS 3.1 15.6 + - - +
40B PRO 3.3 3.9 - - - +
41B GLY* 1.3 75.2 - - - +
43B LEU* 1.3 65.9 + - - +
44B GLY* 3.1 39.5 - - - -
45B PHE* 3.8 19.3 - + + -
80B THR* 4.0 12.8 - - + -
81B VAL 3.9 3.4 - - - -
82B TRP* 3.6 23.9 - + + -
305B GLN* 4.2 12.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU* 4.3 8.3 - - - +
6B PRO* 3.6 31.4 - - + -
40B PRO 5.2 0.7 - - - +
41B GLY 3.7 10.5 - - - +
42B PHE* 1.3 81.5 - - - +
44B GLY* 1.3 58.3 + - - +
81B VAL* 2.8 13.2 + - + +
82B TRP 3.6 12.8 - - - -
83B LYS* 3.7 26.7 - - + +
305B GLN* 3.7 11.5 + - - +
307B LEU* 4.0 3.1 - - - +
308B TRP* 3.2 34.6 + - + -
311B HIS* 3.9 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.1 18.4 - - - -
43B LEU* 1.3 80.4 - - - +
45B PHE* 1.3 62.8 - - - +
81B VAL 2.9 24.7 + - - -
305B GLN* 3.2 24.7 - - - -
308B TRP* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B CSS 3.8 46.9 - - + -
42B PHE* 3.8 19.5 - + + -
44B GLY* 1.3 74.9 - - - +
46B GLU* 1.3 72.7 + - - +
47B GLN* 4.0 10.8 - - + -
79B TYR 3.0 18.8 - - - +
80B THR* 4.2 2.0 - - + -
81B VAL* 4.9 0.9 - - - -
303B MET* 3.7 42.0 - - + -
304B GLU* 3.6 4.6 - - - -
305B GLN* 3.0 58.3 + - + +
308B TRP* 4.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 1.3 81.7 - - - +
47B GLN* 1.3 60.4 + - - +
48B LEU* 4.2 14.4 - - + +
77B PHE 3.6 1.9 - - - +
78B GLN* 3.3 4.3 - - - +
79B TYR* 2.7 66.4 + - + +
158B ARG* 4.5 0.9 + - - -
160B VAL* 6.0 0.7 - - - +
256B HIS* 5.6 3.8 - - + -
258B GLU* 5.5 0.2 - - - -
301B PRO* 4.7 4.0 - - - +
303B MET 3.9 1.8 - - - -
304B GLU* 2.7 33.8 - - - +
306B GLY* 4.7 2.1 - - - -
308B TRP* 3.2 33.4 + - + -
309B ARG* 3.4 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 4.5 25.4 + - - +
29B GLY* 4.8 6.1 - - - -
45B PHE* 4.0 5.9 - - + -
46B GLU* 1.3 70.1 + - - +
48B LEU* 1.3 62.1 + - - +
76B MET* 4.4 18.6 - - - +
77B PHE 3.9 1.8 - - - -
78B GLN* 4.2 24.5 + - + +
300B SER 3.7 0.2 - - - +
301B PRO* 3.4 3.6 - - - +
302B MET* 2.8 53.5 + - + +
303B MET* 2.9 54.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 4.2 18.6 - - + +
47B GLN* 1.3 76.3 - - - +
49B LEU* 1.3 60.9 + - - +
76B MET* 3.4 8.2 - - - +
77B PHE* 2.7 46.3 + - + +
79B TYR* 3.6 35.0 - - + +
160B VAL* 3.9 35.0 - - + -
162B ILE* 4.0 11.9 - - + -
256B HIS* 4.9 1.1 - - + -
299B PHE* 3.6 16.1 - - + -
300B SER 3.6 1.6 - - - -
301B PRO* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 4.2 6.7 - - + -
22B TYR* 3.6 31.2 - - + +
25B MET* 4.5 8.7 - - + -
47B GLN 4.1 0.6 + - - -
48B LEU* 1.3 73.2 - - - +
50B GLN* 1.3 66.6 + - - +
51B THR* 3.4 5.6 + - + +
74B MET* 4.0 31.0 - - + -
75B GLY 3.6 15.3 - - - +
76B MET* 3.7 18.8 - - + -
299B PHE* 3.2 2.6 - - - -
300B SER* 2.8 35.8 + - - +
302B MET* 4.0 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 4.7 3.6 + - - -
49B LEU* 1.3 72.3 - - - +
51B THR* 1.3 63.7 + - - +
52B GLY 3.1 20.4 + - - +
53B ILE* 3.7 16.8 - - - +
71B LEU* 3.4 27.6 - - + +
73B PRO 5.0 0.2 - - - +
74B MET* 3.2 27.4 - - - +
75B GLY* 2.9 43.8 + - - +
295B TYR* 5.3 0.6 + - - -
297B MET* 3.4 30.0 - - + +
298B PHE 3.3 14.8 - - - +
299B PHE* 3.4 9.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.7 12.6 - - + +
50B GLN* 1.3 78.3 - - - +
52B GLY* 1.3 52.1 + - - +
65B VAL 3.4 5.7 + - - +
66B ASP* 3.6 1.8 - - - -
67B MET* 2.7 32.9 + - - -
68B ARG* 3.5 36.5 + - + +
71B LEU* 4.7 2.0 - - - -
159B THR* 5.8 1.0 - - - +
262B PRO* 5.6 5.9 - - - +
298B PHE* 2.8 25.6 + - - +
299B PHE* 3.9 3.3 + - - -
300B SER* 3.9 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLN* 3.1 21.0 + - - +
51B THR* 1.3 82.9 + - - +
53B ILE* 1.3 64.4 + - - +
64B ALA 3.5 6.5 - - - -
65B VAL 3.3 11.2 - - - -
67B MET* 4.1 11.2 - - - -
71B LEU* 4.9 0.7 - - - -
298B PHE* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLN* 3.7 14.6 - - - +
52B GLY* 1.3 78.9 - - - +
54B HIS* 1.3 67.0 + - - +
55B PRO* 3.4 1.0 - - - +
60B TYR* 3.7 30.5 - - + +
63B GLY* 3.8 18.4 - - - -
64B ALA 3.0 32.5 + - - +
65B VAL* 3.3 16.1 + - - +
67B MET* 4.2 8.3 - - + -
71B LEU* 6.3 0.4 - - + -
295B TYR* 3.3 34.1 - - + +
296B TYR 3.3 13.2 - - - +
297B MET* 4.7 0.7 - - - -
298B PHE* 3.7 8.4 - - - -
----------------------------------------------------------
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