Contacts of the helix formed by residues 9 - 22 (chain B) 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 LEU 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B GLY* 1.3 74.2 - - - +
10B THR* 1.3 66.6 + - - +
11B GLU 3.1 2.0 - - - -
12B LEU* 2.9 21.8 + - + +
13B LEU* 2.9 30.7 + - + +
16C TYR* 3.9 21.1 - - + +
17C THR* 3.4 32.3 - - + +
20C VAL* 4.5 19.1 - - + -
21C LEU* 5.5 4.5 - - + -
28C LEU* 5.9 4.0 - - + -
647D MET* 3.3 26.2 - - + -
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 1.3 77.7 - - - +
11B GLU* 1.3 66.9 + - - +
13B LEU* 4.1 0.2 - - - -
14B GLN* 2.9 42.5 + - - +
640D LYS* 6.0 6.5 - - + -
643D VAL* 4.0 26.8 - - + +
644D SER* 5.4 6.5 - - - +
647D MET* 3.5 16.7 - - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 3.4 30.4 + - - +
10B THR* 1.3 85.2 + - - +
12B LEU* 1.3 58.0 + - - +
14B GLN* 3.4 11.6 - - - +
15B GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY 3.7 10.2 + - - +
9B LEU* 2.9 16.5 + - + +
11B GLU* 1.3 75.5 - - - +
13B LEU* 1.3 72.7 + - + +
15B GLY* 3.1 3.9 + - - -
16B TYR* 3.0 19.2 + - - +
35B TYR* 4.8 2.2 + - + +
36B PHE* 3.1 38.4 - - + -
39B LEU* 4.0 13.9 - - + -
16C TYR* 4.0 22.9 - - + +
28C LEU* 4.4 17.9 - - + -
29C VAL* 4.9 12.3 - - + +
32C ALA* 4.9 1.8 - - + -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 2.9 38.8 + - + +
12B LEU* 1.3 83.1 - - + +
14B GLN* 1.3 57.5 + - - +
16B TYR* 3.4 7.0 + - - +
17B THR* 2.8 37.3 + - - +
36B PHE* 5.7 4.5 - - + -
13C LEU* 4.4 24.2 - - + -
16C TYR* 4.4 15.3 - - + -
17C THR* 3.6 21.8 - - - +
643D VAL* 3.5 33.7 - - + -
646D VAL* 4.9 3.6 - - + -
647D MET* 4.4 4.7 - - + -
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 2.9 32.7 + - - +
11B GLU* 3.4 11.9 - - - +
12B LEU 3.1 0.2 - - - -
13B LEU* 1.3 76.2 - - - +
15B GLY* 1.3 64.4 + - - +
17B THR* 3.1 2.7 + - - -
18B VAL* 2.9 27.1 + - - +
636D TRP* 3.1 45.9 - - + -
639D ALA* 4.8 7.5 - - + +
640D LYS* 4.9 15.0 - - - +
643D VAL* 4.1 12.3 - - + +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU 2.9 15.1 + - - -
12B LEU 3.1 2.7 + - - -
14B GLN* 1.3 74.4 - - - +
16B TYR* 1.3 64.1 + - - +
18B VAL* 3.1 12.7 - - - +
19B GLU* 3.0 24.3 + - - +
35B TYR* 3.4 12.8 - - - -
636D TRP* 5.6 1.8 - - - -
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Residues in contact with TYR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU 3.0 12.2 + - - +
13B LEU* 3.7 8.5 - - - +
15B GLY* 1.3 75.0 - - - +
17B THR* 1.3 67.4 + - - +
19B GLU* 2.9 8.1 + - - +
20B VAL* 2.9 48.9 + - + +
28B LEU* 3.8 15.2 + - - +
31B PHE* 3.7 14.9 - + - -
32B ALA* 3.5 37.2 - - + +
35B TYR* 3.4 39.1 + + + -
36B PHE* 3.8 17.5 - + + -
9C LEU* 3.9 18.2 - - + +
12C LEU* 4.4 9.6 - - + +
13C LEU* 4.3 15.0 - - + -
36C PHE* 6.2 0.4 - + - -
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 2.8 27.6 + - - -
14B GLN* 3.7 3.6 - - - -
16B TYR* 1.3 77.9 - - - +
18B VAL* 1.3 63.0 + - - +
20B VAL* 2.8 22.0 + - - +
21B LEU* 2.9 19.3 + - + +
9C LEU* 4.0 19.5 - - + +
13C LEU* 3.8 22.0 - - - +
639D ALA* 4.0 27.4 - - + +
642D ILE* 4.3 11.0 - - + -
643D VAL* 4.3 5.0 - - - +
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLN 2.9 14.1 + - - +
15B GLY* 3.1 18.6 - - - +
17B THR* 1.3 77.6 - - - +
19B GLU* 1.3 78.4 + - - +
21B LEU* 3.4 2.4 + - - +
22B ARG* 3.2 38.1 + - - +
635D ALA* 3.3 25.4 - - - +
636D TRP* 3.3 39.5 - - + +
639D ALA* 4.5 3.7 - - + +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.3 12.3 - - - +
16B TYR 2.9 12.6 + - - +
18B VAL* 1.3 94.1 - - - +
20B VAL* 1.3 59.4 + - - +
22B ARG* 3.7 26.3 + - - +
23B GLN* 3.2 52.7 + - - +
31B PHE* 4.2 7.7 - - + -
35B TYR* 3.9 24.5 - - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 2.9 49.8 + - + +
17B THR* 2.8 16.9 + - - +
19B GLU* 1.3 71.9 - - - +
21B LEU* 1.3 70.2 + - + +
23B GLN* 4.9 0.2 - - - -
24B GLN* 2.8 36.7 + - - +
25B PRO* 5.0 0.9 - - + -
28B LEU* 4.7 13.2 - - + -
31B PHE* 4.1 13.5 - - + -
6C PRO* 4.4 20.2 - - + -
9C LEU* 4.6 15.0 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 2.9 31.1 + - + +
18B VAL 3.8 2.2 - - - +
19B GLU 3.3 0.4 - - - -
20B VAL* 1.3 87.2 - - + +
22B ARG* 1.3 59.0 + - - +
23B GLN 3.2 0.7 - - - -
24B GLN* 3.0 22.5 + - - +
3C ILE* 4.0 19.9 - - + +
4C GLN 3.4 25.4 - - - +
5C ILE* 4.6 11.0 - - + -
6C PRO* 4.6 2.7 - - + -
9C LEU* 5.7 2.7 - - + -
635D ALA* 3.4 41.1 - - + +
638D ILE* 4.0 22.0 - - + -
639D ALA* 4.6 2.9 - - + -
642D ILE* 5.2 1.8 - - + -
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 3.2 30.6 + - + +
19B GLU* 4.1 29.6 + - - +
20B VAL 3.3 0.4 - - - -
21B LEU* 1.3 79.2 - - + +
23B GLN* 1.3 61.7 + - + +
24B GLN* 5.0 0.9 - - - -
635D ALA 5.5 2.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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