Contacts of the helix formed by residues 8 - 22 (chain F) in PDB entry 3TMH
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 8 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F PRO 4.1 0.4 - - - -
7F PRO* 1.3 71.8 - - - +
9F LEU* 1.3 63.0 + - - +
11F GLU* 3.4 23.9 - - - +
12F LEU* 3.7 15.6 + - - +
441I ASP* 2.9 13.7 + - - +
444I GLN* 5.5 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 4.5 6.1 - - + -
6F PRO* 4.0 37.6 + - + +
7F PRO 3.6 0.8 - - - -
8F GLY* 1.3 74.9 - - - +
10F THR* 1.3 62.1 + - - +
11F GLU 3.2 1.8 - - - -
12F LEU* 2.9 27.1 + - + +
13F LEU* 3.0 40.8 + - + +
16G TYR* 4.2 18.4 - - + +
17G THR* 4.0 28.0 - - + +
20G VAL* 4.7 11.7 - - + -
28G LEU* 5.6 7.2 - - + -
647H MET* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 5.3 4.3 - - - +
6F PRO 5.5 1.4 + - - -
8F GLY 4.8 0.2 - - - +
9F LEU* 1.3 78.0 - - - +
11F GLU* 1.3 63.8 + - - +
13F LEU* 3.9 3.2 - - - +
14F GLN* 2.9 39.3 + - + +
643H VAL* 4.8 9.8 - - + +
647H MET* 3.5 25.1 - - + +
441I ASP* 4.6 6.9 + - - -
445I SER* 3.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F GLY* 3.4 17.3 - - - +
9F LEU 3.2 0.2 - - - -
10F THR* 1.3 77.0 + - - +
12F LEU* 1.3 56.0 + - - +
14F GLN* 3.5 8.5 - - - +
15F GLY* 2.9 25.8 + - - -
441I ASP* 2.8 22.7 - - - +
444I GLN* 2.9 43.1 - - + +
445I SER* 2.3 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F GLY 3.7 9.7 + - - +
9F LEU* 2.9 16.1 + - + +
11F GLU* 1.3 75.1 - - - +
13F LEU* 1.3 75.2 + - + +
15F GLY* 3.1 3.5 + - - -
16F TYR* 3.0 19.9 + - - +
35F TYR* 4.8 1.7 + - + +
36F PHE* 3.1 37.7 - - + -
39F LEU* 4.0 13.9 - - + -
16G TYR* 4.6 11.4 - - + +
28G LEU* 4.5 18.8 - - + -
29G VAL* 4.3 20.0 - - + -
32G ALA* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LEU* 3.0 33.0 + - + +
10F THR 4.2 0.7 - - - +
12F LEU* 1.3 83.1 - - + +
14F GLN* 1.3 57.4 + - - +
16F TYR* 3.4 6.3 + - - +
17F THR* 2.7 40.1 + - - +
36F PHE* 5.8 4.3 - - + -
13G LEU* 4.7 19.3 - - + -
16G TYR* 4.5 15.0 - - + -
17G THR* 3.7 21.8 - - - +
643H VAL* 3.9 20.0 - - + -
646H VAL* 5.5 1.3 - - + -
647H MET* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F THR* 2.9 27.3 + - + +
11F GLU* 3.5 7.6 - - - +
13F LEU* 1.3 76.0 - - - +
15F GLY* 1.3 64.8 + - - +
17F THR* 3.0 5.1 + - - -
18F VAL* 2.9 31.4 + - + +
640H LYS* 6.3 6.1 - - + -
643H VAL* 4.6 10.2 - - + +
444I GLN 4.9 1.9 + - - -
445I SER* 2.5 25.0 + - - +
446I SER 4.1 0.2 - - - -
447I GLY* 3.1 37.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLU 2.9 15.7 + - - -
12F LEU 3.1 2.7 + - - -
14F GLN* 1.3 75.9 - - - +
16F TYR* 1.3 64.0 + - - +
18F VAL* 3.1 11.9 - - - +
19F GLU* 3.0 24.5 + - - +
35F TYR* 3.4 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU 3.0 11.9 + - - +
13F LEU* 3.7 7.9 - - - +
15F GLY* 1.3 76.8 - - - +
17F THR* 1.3 73.4 + - - +
19F GLU* 2.9 6.6 + - - +
20F VAL* 2.9 44.6 + - + +
28F LEU* 3.9 11.3 + - - +
31F PHE* 3.9 17.2 - + - -
32F ALA* 3.5 37.4 - - + +
35F TYR* 3.4 32.2 + + + -
36F PHE* 3.7 25.4 - + + -
9G LEU* 4.0 15.8 - - + +
12G LEU* 4.2 11.9 - - + +
13G LEU* 4.3 12.8 - - + -
36G PHE* 6.0 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU 2.7 27.0 + - - -
14F GLN* 3.7 2.5 - - - -
16F TYR* 1.3 81.2 - - - +
18F VAL* 1.3 56.4 + - - +
20F VAL* 2.7 25.7 + - - +
21F LEU* 3.0 25.8 + - + +
9G LEU* 3.6 22.6 - - + +
13G LEU* 3.5 21.7 - - - +
640H LYS 5.5 4.5 - - - +
642H ILE* 4.8 8.3 - - + -
643H VAL* 3.7 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLN* 2.9 17.7 + - + +
15F GLY* 3.1 19.1 - - - +
17F THR* 1.3 77.8 - - - +
19F GLU* 1.3 77.8 + - + +
21F LEU* 3.4 12.7 + - + +
22F ARG* 3.3 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F GLY 3.0 11.6 + - - +
16F TYR 2.9 12.8 + - - +
18F VAL* 1.3 95.4 - - + +
20F VAL* 1.3 62.5 + - - +
22F ARG* 3.6 26.2 + - - +
23F GLN* 3.2 50.3 + - - +
31F PHE* 4.3 7.7 - - + -
35F TYR* 3.8 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F TYR* 2.9 50.3 + - + +
17F THR* 2.7 15.8 + - - +
19F GLU* 1.3 71.9 - - - +
21F LEU* 1.3 69.6 + - + +
23F GLN* 4.9 0.4 - - - -
24F GLN* 2.8 42.4 + - + +
25F PRO* 5.0 0.7 - - + -
28F LEU* 4.7 13.0 - - + -
31F PHE* 4.1 13.0 - - + -
9G LEU* 4.4 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F THR* 3.0 24.3 + - + +
18F VAL* 3.4 14.3 + - + +
19F GLU 3.3 0.2 - - - -
20F VAL* 1.3 90.0 - - + +
22F ARG* 1.3 61.1 + - + +
23F GLN 3.2 0.4 - - - -
24F GLN* 3.0 29.9 + - + +
9G LEU* 5.2 2.2 - - + -
640H LYS 5.9 4.5 - - - +
642H ILE* 4.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL* 3.3 31.1 + - + +
19F GLU* 4.1 27.1 + - - +
20F VAL 3.3 0.6 - - - -
21F LEU* 1.3 77.6 - - + +
23F GLN* 1.3 65.6 + - + +
24F GLN* 5.0 1.3 - - - -
----------------------------------------------------------
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