Contacts of the strand formed by residues 19 - 28 (chain B) in PDB entry 2QVH
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 ILE 19 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU* 3.3 13.2 - - - +
12B LEU* 3.5 12.8 - - + +
15B ARG* 3.4 4.4 - - - -
16B PHE 3.0 39.1 + - - +
17B ARG* 3.9 18.6 - - + +
18B GLY* 1.3 84.4 - - - +
20B THR* 1.3 63.7 - - - +
21B VAL 3.6 21.1 - - - +
22B ARG* 3.8 16.4 - - - -
39B PHE* 3.7 31.6 - - + -
230B VAL* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU 4.8 2.6 + - - -
217A ALA 5.6 0.9 - - - +
218A GLU* 2.8 38.7 + - + +
247A PRO* 4.4 27.9 - - + +
11B PRO* 3.6 2.4 - - - +
12B LEU* 2.9 34.7 + - - +
15B ARG* 4.0 28.0 - - + +
19B ILE* 1.3 78.8 - - - +
21B VAL* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 6.3 4.5 - - + -
218A GLU* 3.5 10.5 + - - +
9B ALA* 4.2 16.4 - - + -
10B ILE 3.5 24.2 - - - +
11B PRO* 4.3 7.6 - - + -
12B LEU* 3.5 4.4 - - - +
19B ILE* 3.6 17.2 - - - +
20B THR* 1.3 97.0 - - - +
22B ARG* 1.3 63.9 + - - +
23B GLU* 3.8 13.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.4 16.7 - - + -
10B ILE* 2.7 43.9 + - + +
12B LEU* 3.4 2.4 - - + +
19B ILE* 3.8 18.8 - - - +
21B VAL* 1.3 72.8 - - - +
23B GLU* 1.3 83.2 + - - +
35B GLU* 5.1 0.2 - - - -
37B SER* 2.9 44.4 + - - -
38B PRO 4.8 1.4 + - - -
39B PHE* 3.5 26.3 - - - +
50B TRP* 4.3 0.4 - - - -
229B ALA* 2.8 27.6 + - - +
230B VAL* 2.8 34.3 + - - +
231B GLU* 4.5 2.4 - - - +
232B THR 5.9 0.2 - - - +
261B LEU* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.3 16.4 - - - +
9B ALA* 3.9 14.6 - - + +
21B VAL* 3.8 15.1 + - + +
22B ARG* 1.3 98.9 + - - +
24B GLY* 1.3 58.9 + - - +
37B SER* 3.5 3.5 - - - -
38B PRO 4.8 0.3 - - - +
294B ILE* 4.1 11.2 - - - +
299B TRP* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA* 3.3 7.1 - - - +
8B PHE* 2.9 44.6 + - - +
23B GLU* 1.3 77.7 - - - +
25B MSE 1.3 59.8 - - - -
36B PHE 3.4 11.4 - - - -
37B SER* 3.8 1.6 - - - -
299B TRP* 3.6 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLY* 4.0 11.7 - - - +
6B ARG 3.3 14.1 - - - +
7B ALA 3.8 9.4 - - - +
8B PHE* 3.6 0.6 - - - -
24B GLY* 1.3 75.9 - - - -
26B LEU* 1.3 70.9 + - - +
27B VAL* 4.3 1.1 - - + -
34B GLY 3.9 0.2 - - - +
35B GLU* 3.5 4.5 - - - +
36B PHE* 2.8 44.8 + - + +
54B CYS* 4.9 0.3 - - - -
296B PRO* 3.6 17.0 - - + -
299B TRP* 3.5 34.8 - - + +
300B GLN* 3.4 40.4 - - + -
303B LEU* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR 3.7 2.8 - - - +
5B GLY* 3.4 4.3 - - - -
6B ARG* 2.8 33.1 + - + +
8B PHE* 3.8 24.7 - - + -
25B MSE 1.3 73.4 - - - +
27B VAL* 1.3 60.8 + - - +
33B TRP* 3.9 17.9 - - + -
34B GLY 3.3 1.6 - - - -
35B GLU* 4.0 12.6 - - + -
232B THR* 4.1 4.0 - - - +
234B VAL* 3.9 30.7 - - + -
265B VAL* 4.0 23.6 - - + -
284B VAL* 4.6 8.5 - - + -
289B LEU* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 4.4 6.7 - - - -
5B GLY* 4.3 10.8 - - - +
25B MSE 4.3 6.3 - - + -
26B LEU* 1.3 79.7 - - - +
28B ARG* 1.3 68.4 + - - +
29B GLY* 5.6 0.4 - - - -
33B TRP* 3.4 4.8 - - - -
34B GLY 2.8 34.6 + - - -
51B TRP* 4.5 12.1 - - + -
54B CYS* 3.9 24.5 - - - -
58B ALA* 3.3 14.2 - - + +
303B LEU* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU 6.1 0.2 - - - +
4B THR* 4.4 14.0 + - - +
27B VAL* 1.3 80.4 - - - +
29B GLY* 1.3 87.8 + - - +
30B ALA* 4.6 4.0 + - - +
31B ALA 4.8 0.4 - - - -
32B GLY* 3.5 18.8 - - - +
33B TRP* 3.3 56.7 - - + +
----------------------------------------------------------
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