Contacts of the helix formed by residues 9 - 26 (chain H) in PDB entry 2D2C
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H GLY* 3.1 26.5 - - - +
6H TRP* 2.5 26.0 + - + +
7H VAL 2.4 13.5 + - - +
8H ALA* 1.3 80.1 - - + +
10H LEU* 1.3 58.5 + - - +
11H VAL 2.4 18.4 + - - -
12H VAL 2.7 12.8 + - - -
13H PHE* 3.1 39.1 + - + -
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Residues in contact with LEU 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ILE* 6.3 2.9 - - + -
262C ILE* 5.7 4.0 - - + -
263C CYS* 5.0 15.3 - - - -
266C MET* 4.3 17.7 - - + -
8G LEU* 5.8 10.8 - - + -
11G ALA 4.4 16.4 - - - +
12G THR* 4.4 13.2 - - + +
15G GLY* 4.1 13.7 - - - +
6H TRP* 3.0 6.9 + - + +
7H VAL* 5.6 0.2 - - - -
9H LEU* 1.3 77.9 - - - +
11H VAL* 1.3 69.7 + - + +
13H PHE* 3.0 31.7 + - + +
14H THR* 3.2 19.6 + - - +
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Residues in contact with VAL 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C MET* 5.7 0.9 - - - -
19F VAL* 5.7 2.9 - - + -
23F LEU* 4.5 21.3 - - + -
15G GLY* 3.3 28.5 - - - +
18G TYR* 4.9 10.8 - - + -
21G TYR* 4.9 13.5 - - + -
7H VAL* 2.9 47.3 - - + +
8H ALA* 5.9 0.2 - - - -
9H LEU 2.4 5.9 + - - -
10H LEU* 1.3 76.9 - - + +
12H VAL* 1.3 72.4 + - + +
14H THR* 3.0 14.9 + - - -
15H TRP* 3.2 8.3 + - + +
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 6.3 2.0 - - + -
8H ALA* 2.8 32.3 - - + +
9H LEU 2.7 5.5 + - - -
11H VAL* 1.3 83.7 - - + +
13H PHE* 1.3 56.5 + - + +
15H TRP* 2.7 31.7 + - + +
16H SER* 2.5 39.6 + - - +
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Residues in contact with PHE 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ALA 4.3 3.4 - - - -
9H LEU* 3.1 57.0 - - + -
10H LEU* 3.0 27.1 + - + +
12H VAL* 1.3 82.7 - - + +
14H THR* 1.3 55.1 + - - +
16H SER* 3.7 13.8 + - - -
17H ILE* 3.1 23.0 - - - +
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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
----------------------------------------------------------
266C MET* 3.8 40.0 - - + +
267C LEU* 4.4 14.8 - - + -
270C LEU* 5.4 5.4 - - + +
18G TYR* 4.2 20.5 + - + +
10H LEU* 3.2 19.8 + - - +
11H VAL 3.0 7.3 + - - -
13H PHE* 1.3 73.9 - - - +
15H TRP* 1.3 66.8 + - - +
16H SER 3.1 0.9 - - - -
17H ILE* 3.1 25.5 + - + +
18H ALA* 3.1 12.0 + - - +
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Residues in contact with TRP 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 4.4 22.4 - - + +
26F LEU* 3.2 48.5 - - + -
27F LEU* 2.7 34.7 - - + +
30F ILE* 5.0 6.3 - - + -
18G TYR* 4.8 13.2 - + + -
11H VAL* 3.2 6.8 + - + +
12H VAL* 2.7 39.7 + - + +
14H THR* 1.3 78.0 - - - +
16H SER* 1.3 50.4 + - - +
17H ILE 2.7 1.9 + - - -
18H ALA* 2.7 37.4 + - + +
19H MET* 3.2 37.0 + - + +
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Residues in contact with SER 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 2.5 23.5 + - - +
13H PHE* 3.7 15.0 - - - -
14H THR 3.1 0.6 - - - -
15H TRP* 1.3 71.1 - - - +
17H ILE* 1.3 60.7 + - - +
19H MET* 3.9 14.4 - - - +
20H VAL* 3.0 21.8 - - - +
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Residues in contact with ILE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 5.4 9.2 - - + -
270C LEU* 5.6 0.9 - - - -
13H PHE 3.1 22.2 - - - +
14H THR* 3.4 20.9 - - + +
15H TRP 2.9 0.2 - - - -
16H SER* 1.3 79.8 - - - +
18H ALA* 1.3 61.5 - - - +
20H VAL* 3.4 6.8 - - - +
21H VAL* 3.0 43.5 + - + +
24H ARG* 5.3 9.2 - - - +
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Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 4.6 15.2 - - + +
27F LEU* 6.3 1.6 - - + -
18G TYR* 4.2 13.0 - - - +
14H THR 3.1 11.4 + - - +
15H TRP* 2.7 21.7 + - + +
17H ILE* 1.3 73.6 - - - +
19H MET* 1.3 64.2 + - - +
20H VAL 2.9 3.8 - - - -
21H VAL* 2.5 32.6 - - - +
22H TRP* 3.8 2.1 + - - +
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Residues in contact with MET 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ILE* 4.9 21.7 - - + +
15H TRP* 3.3 46.9 - - + +
16H SER* 3.9 12.8 - - - +
18H ALA* 1.3 76.1 - - + +
20H VAL* 1.3 87.6 + - - +
22H TRP* 3.7 17.8 + - - +
23H GLY* 3.8 5.7 + - - -
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H SER* 3.0 28.7 - - - +
17H ILE* 3.4 10.3 - - - +
18H ALA 2.9 0.6 + - - -
19H MET* 1.3 89.4 - - - +
21H VAL* 1.3 58.1 + - - +
23H GLY* 2.9 25.3 + - - -
24H ARG* 3.6 30.6 + - + +
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Residues in contact with VAL 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C LEU* 5.4 4.0 - - + -
271C MET* 6.5 0.2 - - - -
274C LEU* 4.2 32.8 - - + -
17H ILE* 3.0 25.0 + - + +
18H ALA* 2.5 37.2 + - - +
20H VAL* 1.3 68.1 - - - +
22H TRP* 1.3 66.5 + - - +
24H ARG* 2.9 42.3 + - - +
25H ASN* 3.0 16.3 - - - +
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Residues in contact with TRP 22 (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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30F ILE* 5.7 10.3 - - + -
31F GLN* 6.1 6.3 - - + -
18H ALA 3.8 1.1 + - - +
19H MET* 3.7 13.8 + - - +
20H VAL 3.3 1.2 - - - -
21H VAL* 1.3 81.2 - - - +
23H GLY* 1.3 78.7 + - - +
24H ARG 2.6 12.5 + - - -
25H ASN* 2.9 13.9 + - - +
26H GLY* 2.9 52.5 + - - -
27H LEU* 3.5 36.6 - - + -
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Residues in contact with GLY 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 MET 3.8 0.9 + - - -
20H VAL 2.9 12.9 + - - -
22H TRP* 1.3 103.8 - - - +
24H ARG* 1.3 50.1 + - - +
27H LEU* 2.4 39.8 - - - +
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Residues in contact with ARG 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ILE* 5.3 8.5 - - - +
20H VAL* 3.9 29.9 - - + +
21H VAL* 2.9 36.0 + - - +
22H TRP 2.6 6.3 + - - -
23H GLY* 1.3 74.4 - - - +
25H ASN* 1.3 56.2 + - - +
27H LEU* 2.7 22.1 - - - +
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Residues in contact with ASN 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 VAL* 3.0 15.8 - - - +
22H TRP* 2.9 19.0 + - - +
24H ARG* 1.3 76.4 - - - +
26H GLY* 1.3 74.4 + - - +
27H LEU* 2.9 6.4 + - - +
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Residues in contact with GLY 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H TRP* 2.9 37.8 + - - -
25H ASN* 1.3 81.5 - - - +
27H LEU* 1.3 66.7 + - - +
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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
------------------------------------------------------------
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