Contacts of the helix formed by residues 8 - 25 (chain A) in PDB entry 6Q3W
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 GLN 8 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN 3.4 3.9 + - - -
7A PRO* 1.3 77.8 - - - +
9A VAL* 1.3 67.6 + - + +
10A ALA* 3.0 10.8 - - + +
11A GLU* 3.0 20.8 + - + +
12A LEU* 3.2 9.9 + - - +
60A MET* 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO 3.8 0.4 + - - -
8A GLN* 1.3 73.4 - - + +
10A ALA* 1.3 62.0 + - + +
12A LEU* 3.5 3.0 + - - +
13A LEU* 2.8 37.5 + - + +
33A SER* 4.1 18.4 - - - +
60A MET* 3.7 38.4 - - + +
62A VAL* 4.3 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 3.0 8.2 - - + +
9A VAL* 1.3 85.9 - - + +
11A GLU* 1.3 57.1 + - - +
13A LEU* 3.5 12.4 - - - +
14A ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.8 31.8 - - + +
8A GLN* 3.0 15.9 + - + +
10A ALA* 1.3 76.7 - - - +
12A LEU* 1.3 60.3 + - + +
14A ALA* 3.3 7.1 + - - +
15A GLU* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 4.0 27.8 - - + +
8A GLN 3.2 6.3 + - - +
9A VAL 4.0 3.4 - - - +
11A GLU* 1.3 74.3 - - + +
13A LEU* 1.3 60.5 + - - +
15A GLU* 3.4 19.7 + - - +
16A ALA* 2.9 31.4 + - - +
60A MET* 3.6 38.1 - - + +
62A VAL* 3.9 16.2 - - + -
130A VAL* 3.7 15.7 - - + +
131A SER 4.6 9.2 - - - +
132A SER* 3.6 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 2.8 24.9 + - + +
10A ALA* 3.5 11.2 - - + +
12A LEU* 1.3 77.3 - - - +
14A ALA* 1.3 51.7 + - - +
16A ALA* 3.2 1.6 + - - +
17A ARG* 2.8 56.6 + - + +
31A ALA* 3.6 27.4 - - + -
62A VAL* 4.4 11.3 - - + +
64A VAL* 3.7 12.6 - - + -
390A LEU* 3.6 29.8 - - + -
392A LEU* 4.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 2.9 18.1 + - - +
11A GLU* 3.6 6.7 - - - +
13A LEU* 1.3 76.6 - - - +
15A GLU* 1.3 63.1 + - - +
17A ARG* 3.8 7.4 - - - +
18A ARG* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.0 16.9 + - + +
12A LEU* 3.7 23.0 - - - +
14A ALA* 1.3 77.5 - - - +
16A ALA* 1.3 62.6 + - - +
18A ARG* 4.0 4.1 - - - +
19A ALA* 3.1 24.8 + - + +
78A THR* 3.1 29.6 + - + +
130A VAL* 4.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU 2.9 18.4 + - - +
13A LEU 3.6 3.1 - - - +
15A GLU* 1.3 75.9 - - - +
17A ARG* 1.3 59.1 + - - +
19A ALA* 3.4 2.1 + - - +
20A PHE* 2.9 24.1 + - - +
62A VAL* 4.3 4.3 - - + -
64A VAL* 3.3 35.3 - - + +
128A VAL* 4.0 8.4 - - + +
130A VAL* 3.9 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 2.8 40.9 + - + +
14A ALA* 3.8 6.5 - - - +
16A ALA* 1.3 77.6 - - - +
18A ARG* 1.3 57.4 + - - +
20A PHE* 3.3 2.4 + - - +
21A ARG* 2.9 29.9 + - - +
27A GLU* 3.1 39.0 + - - +
28A PRO* 3.9 18.4 + - + +
64A VAL* 4.3 1.8 - - + -
392A LEU* 3.5 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.0 17.2 + - - +
15A GLU* 4.0 4.7 - - - +
17A ARG* 1.3 73.0 - - - +
19A ALA* 1.3 66.3 + - - +
21A ARG* 3.4 7.4 + - - +
22A GLU* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.1 19.7 + - + +
16A ALA 3.6 4.3 - - - +
18A ARG* 1.3 77.1 - - - +
20A PHE* 1.3 57.7 + - - +
22A GLU* 3.4 4.9 + - - +
23A GLU* 2.9 31.1 + - - +
76A LEU* 4.6 5.5 - - + +
78A THR* 4.1 18.2 - - + -
128A VAL* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 2.9 18.4 + - - +
17A ARG 3.3 4.7 + - - +
19A ALA* 1.3 76.5 - - - +
21A ARG* 1.3 56.6 + - - +
23A GLU* 3.1 1.7 + - - +
24A PHE* 2.8 67.8 + + + +
26A ALA* 3.2 23.1 - - + -
27A GLU 4.1 2.9 - - - -
28A PRO* 3.6 22.2 - - + -
64A VAL* 3.8 21.3 - - + -
65A GLY* 3.5 7.6 - - - -
66A SER* 3.7 18.6 - - - -
126A SER* 3.4 31.9 - - - -
128A VAL* 3.6 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG 2.9 17.5 + - - +
18A ARG* 3.7 8.1 - - - +
20A PHE* 1.3 76.5 - - - +
22A GLU* 1.3 58.2 + - - +
25A GLY* 3.0 47.3 + - - -
26A ALA* 3.3 27.7 - - - +
27A GLU* 3.7 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG 3.1 15.5 + - - +
19A ALA* 3.9 5.4 - - - +
21A ARG* 1.3 80.7 - - - +
23A GLU* 1.3 63.1 + - - +
25A GLY* 4.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.9 19.1 + - - +
20A PHE* 3.1 3.5 + - - +
22A GLU* 1.3 80.3 - - - +
24A PHE* 1.3 92.8 + - + +
75A LEU 5.6 0.2 - - - +
76A LEU* 3.7 19.7 - - + +
87A ARG* 2.4 44.1 + - - +
89A GLN* 5.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 2.8 63.5 + + + +
23A GLU* 1.3 100.4 - - + +
25A GLY* 1.3 60.4 + - - +
26A ALA* 3.1 9.2 + - + +
68A ARG* 4.7 4.9 - - - -
74A SER* 3.3 35.4 - - - -
75A LEU 5.0 3.4 - - - -
76A LEU* 5.2 0.7 - - + -
126A SER* 3.5 25.8 - - - -
127A ALA 4.1 11.4 - - - -
128A VAL* 4.1 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 3.0 36.7 + - - -
22A GLU 4.3 3.2 + - - -
23A GLU 3.6 1.8 - - - -
24A PHE* 1.3 77.7 - - - +
26A ALA* 1.3 59.4 + - - +
----------------------------------------------------------
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