Contacts of the helix formed by residues 7 - 30 (chain H) in PDB entry 5VOT
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 7 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ARG* 1.3 77.6 - - - +
8H VAL* 1.3 57.4 + - - +
9H GLN 3.0 0.4 - - - -
10H MET* 2.8 37.2 + - - +
11H LEU* 2.9 12.9 + - - +
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Residues in contact with VAL 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG 3.5 21.5 - - - +
7H GLY* 1.3 76.3 - - - +
9H GLN* 1.3 59.3 + - + +
11H LEU* 3.7 8.3 - - - +
12H LEU* 2.9 33.8 + - - +
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Residues in contact with GLN 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG 3.0 14.4 + - - +
8H VAL* 1.3 81.2 - - + +
10H MET* 1.3 66.6 + - + +
12H LEU* 4.3 2.9 - - - +
13H THR* 2.1 41.6 + - - +
196H LEU* 5.1 11.4 - - + +
200H MET* 4.3 20.4 - - + -
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Residues in contact with MET 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG 5.3 0.9 - - - +
7H GLY* 2.8 25.3 + - - +
9H GLN* 1.3 86.4 - - + +
11H LEU* 1.3 63.3 + - - +
13H THR* 3.2 9.7 + - + +
14H THR* 2.9 33.0 + - + +
122H ILE* 6.1 4.3 - - + -
126H GLU* 6.3 3.8 - - - -
200H MET* 5.5 5.8 - - + -
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Residues in contact with LEU 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H GLY 2.9 10.5 + - - +
8H VAL* 3.3 11.4 + - - +
10H MET* 1.3 74.7 - - - +
12H LEU* 1.3 68.9 + - + +
14H THR* 2.9 23.5 + - - +
15H VAL* 2.9 34.2 + - + +
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H VAL 2.9 19.8 + - - +
9H GLN* 4.3 2.9 - - - +
11H LEU* 1.3 77.3 - - + +
13H THR* 1.3 58.2 + - - +
15H VAL* 3.3 11.9 - - + +
16H GLY* 2.9 26.0 + - - -
193H VAL* 4.6 8.1 - - - +
196H LEU* 5.0 13.7 - - + -
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Residues in contact with THR 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H GLN* 2.1 30.8 + - - +
10H MET* 3.3 13.0 - - + +
12H LEU* 1.3 78.2 - - - +
14H THR* 1.3 60.7 + - + +
16H GLY* 3.6 0.9 - - - -
17H ALA* 2.9 25.5 + - + +
122H ILE* 3.5 45.4 - - + +
193H VAL* 5.0 14.2 + - + +
196H LEU* 5.3 6.5 - - - +
197H ALA* 5.5 10.1 - - + -
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Residues in contact with THR 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H MET* 2.9 21.1 + - + +
11H LEU* 2.9 16.3 + - - +
13H THR* 1.3 78.9 - - + +
15H VAL* 1.3 69.5 + - - +
17H ALA* 2.8 24.0 + - - +
18H PHE* 2.9 25.0 + - - +
122H ILE* 5.8 3.8 - - + -
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Residues in contact with VAL 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU* 2.9 45.1 + - + +
12H LEU* 3.3 15.7 - - - +
14H THR* 1.3 84.5 + - - +
16H GLY* 1.3 52.9 + - - +
18H PHE* 5.2 3.1 - - - -
19H ALA* 2.5 41.7 + - - +
189H ILE* 5.7 0.2 - - - -
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Residues in contact with GLY 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H LEU 2.9 17.0 + - - -
13H THR 3.6 3.6 - - - -
15H VAL* 1.3 76.3 - - - +
17H ALA* 1.3 65.9 + - - +
19H ALA* 4.1 3.8 - - - -
20H ALA* 2.9 28.4 + - - +
142H PHE* 5.2 4.3 - - - -
189H ILE* 4.4 12.3 - - - -
190H ALA* 6.0 0.2 - - - -
193H VAL* 4.3 17.3 - - - -
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Residues in contact with ALA 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H THR* 2.9 13.0 + - + +
14H THR* 2.8 18.6 + - - +
16H GLY* 1.3 71.0 - - - +
18H PHE* 1.3 65.3 + - + +
21H PHE* 2.8 36.5 + - - +
115H LEU* 6.2 0.2 - - - +
119H GLY* 4.4 23.8 - - - +
122H ILE* 5.5 5.8 - - + -
142H PHE* 5.6 7.8 - - - -
193H VAL* 5.4 0.2 - - - +
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Residues in contact with PHE 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H THR* 2.9 22.4 + - - +
15H VAL* 4.7 2.7 - - - +
17H ALA* 1.3 81.7 - - + +
19H ALA* 1.3 63.5 + - - +
21H PHE* 4.2 11.0 - + + -
22H SER* 2.9 33.4 + - - +
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 2.5 26.1 + - + +
16H GLY* 3.8 4.0 - - - +
17H ALA 3.2 0.2 - - - -
18H PHE* 1.3 77.5 - - - +
20H ALA* 1.3 58.6 + - - +
22H SER* 4.3 0.7 - - - -
23H LEU* 2.9 32.8 + - - +
189H ILE* 4.6 12.1 - - + -
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Residues in contact with ALA 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLY 2.9 18.3 + - - +
17H ALA 4.7 0.2 - - - +
19H ALA* 1.3 76.4 - - - +
21H PHE* 1.3 57.5 + - - +
23H LEU 3.8 0.2 - - - -
24H MET* 2.9 29.6 + - - +
115H LEU* 4.0 12.7 - - + +
142H PHE* 5.7 0.9 - - + -
186H SER* 3.3 38.9 - - - +
189H ILE* 5.0 2.9 - - + +
190H ALA* 3.9 19.1 - - + +
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Residues in contact with PHE 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ALA 2.8 24.5 + - - +
18H PHE* 3.9 9.2 - + - +
20H ALA* 1.3 74.8 - - - +
22H SER* 1.3 73.2 + - - +
24H MET* 3.0 5.4 + - + +
25H THR* 2.9 34.5 + - - -
112H VAL* 4.3 16.2 - - + -
115H LEU* 4.0 28.4 - - + +
116H PHE* 4.0 39.9 - + + -
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Residues in contact with SER 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H PHE* 2.9 26.3 + - - +
19H ALA* 4.3 0.7 - - - -
21H PHE* 1.3 79.9 - - - +
23H LEU* 1.3 57.6 + - - +
25H THR* 3.2 8.8 + - - -
26H ILE* 2.9 43.4 + - - +
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Residues in contact with LEU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ALA 2.9 22.2 + - - +
22H SER* 1.3 78.7 - - - +
24H MET* 1.3 56.8 + - - +
26H ILE* 3.6 9.3 + - - +
27H ALA* 2.9 27.5 + - - +
182H PHE* 4.0 17.5 - - + +
186H SER* 3.5 25.1 - - - -
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Residues in contact with MET 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H ALA 2.9 20.2 + - - +
21H PHE* 3.0 4.5 + - + +
23H LEU* 1.3 75.2 - - - +
25H THR* 1.3 59.4 + - - +
27H ALA* 3.2 8.9 + - - +
28H VAL* 2.9 32.9 + - - +
111H SER* 5.3 4.9 - - - +
112H VAL* 5.2 11.9 - - + -
115H LEU* 4.1 17.5 - - + -
183H GLY* 5.3 1.1 - - - -
186H SER* 4.2 6.5 - - - -
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Residues in contact with THR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H PHE* 2.9 29.3 + - - -
22H SER* 3.5 11.5 - - - -
24H MET* 1.3 75.5 - - - +
26H ILE* 1.3 58.1 + - + +
28H VAL* 2.7 32.0 + - + +
29H GLY* 2.9 8.7 + - - -
112H VAL* 5.8 6.2 - - - +
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Residues in contact with ILE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H SER* 2.9 32.7 + - - +
23H LEU* 3.9 7.2 - - - +
25H THR* 1.3 74.5 - - + +
27H ALA* 1.3 56.2 + - - +
29H GLY* 2.7 25.0 + - - +
30H THR 3.5 9.4 + - - +
179H SER* 3.8 19.0 - - - +
182H PHE* 5.4 4.9 - - + -
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Residues in contact with ALA 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LEU 2.9 16.0 + - - +
24H MET* 3.2 14.1 - - - +
25H THR 3.1 0.2 - - - -
26H ILE* 1.3 76.7 - - - +
28H VAL* 1.3 61.7 + - + +
29H GLY 3.4 0.2 + - - -
30H THR 3.9 9.5 + - - +
32H TYR* 4.9 9.0 - - - +
62H GLY* 5.3 2.3 - - - +
179H SER* 3.6 27.4 - - - +
180H PHE* 5.5 0.9 - - - -
182H PHE* 5.4 0.2 - - - +
183H GLY* 3.8 16.8 - - - -
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Residues in contact with VAL 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H MET 2.9 21.1 + - - +
25H THR* 2.7 20.1 + - + +
27H ALA* 1.3 73.1 - - + +
29H GLY* 1.3 62.5 + - - +
62H GLY 4.4 10.7 - - - +
64H TRP* 3.9 40.6 - - + -
108H PRO* 5.7 9.0 - - + -
109H ILE* 6.1 4.9 - - + -
112H VAL* 4.5 19.1 - - + -
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Residues in contact with GLY 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H THR 2.9 7.0 + - - -
26H ILE* 2.7 14.0 + - - -
27H ALA 4.5 0.2 - - - -
28H VAL* 1.3 82.0 - - - +
30H THR* 1.3 70.0 + - - +
62H GLY* 4.8 6.0 - - - +
64H TRP* 6.0 0.7 - - - -
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Residues in contact with THR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ILE* 3.5 4.9 + - - +
27H ALA 3.9 6.8 - - - +
29H GLY* 1.3 83.9 - - - +
31H ASP* 1.3 73.1 + - - +
32H TYR* 3.3 5.2 + - - -
60H HIS* 6.5 0.2 - - - -
61H SER 6.0 0.4 - - - -
62H GLY* 4.6 10.1 - - - +
67H CYS* 6.1 4.3 - - - -
179H SER* 3.2 18.4 + - - -
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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
------------------------------------------------------------
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