Contacts of the helix formed by residues 6 - 18 (chain H) in PDB entry 5A31
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 GLU 6 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458F ALA* 6.2 0.8 - - - +
5H GLN* 1.3 87.6 - - + +
7H PRO* 1.3 76.1 - - - +
8H VAL* 3.2 2.8 + - - -
9H GLN* 3.3 36.0 + - + +
10H ALA* 3.1 18.9 + - - +
39H GLU* 4.1 14.7 - - - +
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Residues in contact with PRO 7 (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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147F PHE* 4.6 10.4 - - + -
455F GLN* 3.7 38.8 - - + +
458F ALA* 5.1 8.3 - - + -
459F ALA* 3.9 24.7 - - + +
5H GLN* 3.5 9.4 - - - +
6H GLU* 1.3 89.9 - - - +
8H VAL* 1.3 57.0 + - + +
10H ALA* 3.3 6.6 + - + +
11H ALA* 2.8 36.9 + - - +
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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
----------------------------------------------------------
147F PHE* 3.5 31.9 - - + -
459F ALA* 4.6 11.2 - - + -
462F LEU* 3.7 31.4 - - + -
6H GLU 3.2 1.1 - - - -
7H PRO* 1.3 77.0 - - + +
9H GLN* 1.3 64.8 + - - +
11H ALA* 3.2 4.1 + - - +
12H ILE* 3.1 28.4 + - + +
27H LEU* 3.5 24.4 - - + +
31H LEU* 3.8 21.5 - - + -
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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 GLU* 3.3 35.2 + - + +
8H VAL* 1.3 82.1 - - - +
10H ALA* 1.3 63.5 + - + +
12H ILE* 3.2 16.2 + - - +
13H TRP* 3.1 40.4 + - + +
31H LEU* 4.4 15.4 - - + +
39H GLU* 3.7 32.9 + - - +
43H LEU* 4.3 9.3 - - + +
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Residues in contact with ALA 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H GLN 5.0 4.0 - - - +
6H GLU 3.1 13.6 + - - +
7H PRO* 3.7 9.6 - - + +
9H GLN* 1.3 78.6 - - + +
11H ALA* 1.3 57.9 + - - +
13H TRP* 3.1 10.7 + - - +
14H GLN* 2.9 29.3 + - - +
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Residues in contact with ALA 11 (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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116F PHE* 4.9 1.9 - - - -
145F ASN* 5.8 4.0 - - - +
147F PHE* 4.3 28.9 - - + -
148F LEU* 5.5 4.6 - - + +
7H PRO 2.8 20.0 + - - +
8H VAL 3.2 5.8 + - - +
10H ALA* 1.3 73.6 - - - +
12H ILE* 1.3 55.0 + - - +
14H GLN* 3.3 14.2 + - - +
15H ALA* 2.9 28.6 + - - +
27H LEU* 4.7 8.3 - - + -
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Residues in contact with ILE 12 (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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8H VAL* 3.1 19.9 + - + +
9H GLN* 3.4 9.4 - - - +
11H ALA* 1.3 73.4 - - - +
13H TRP* 1.3 59.5 + - - +
15H ALA* 3.1 8.5 + - - +
16H LEU* 2.8 27.5 + - + +
24H ALA* 3.7 17.2 - - + +
27H LEU* 3.8 31.0 - - + +
28H ALA* 3.5 27.1 - - + +
31H LEU* 4.4 4.0 - - + -
43H LEU* 3.3 40.6 - - + -
47H CYS* 3.9 8.5 - - - -
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Residues in contact with TRP 13 (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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17F ASN* 4.9 14.4 - - - -
9H GLN* 3.1 42.5 + - + +
10H ALA* 3.1 10.1 + - - +
12H ILE* 1.3 75.2 - - - +
14H GLN* 1.3 62.7 + - - +
16H LEU* 3.3 19.5 + - + +
17H ASN* 3.0 38.5 + - - +
42H PHE* 4.5 23.3 - + - -
43H LEU* 4.1 24.1 - - + +
46H THR* 4.5 11.9 - - + -
50H ARG* 3.7 26.7 - - - -
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Residues in contact with GLN 14 (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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112F ASP* 3.4 31.4 + - - +
115F CYS* 4.5 2.4 - - - -
116F PHE* 3.2 27.5 - - + -
145F ASN* 4.5 14.4 + - - +
10H ALA 2.9 13.6 + - - +
11H ALA* 3.4 15.8 - - - +
13H TRP* 1.3 76.9 - - - +
15H ALA* 1.3 61.7 + - - +
17H ASN* 3.2 7.2 + - - +
18H HIS* 3.0 37.7 + - + +
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Residues in contact with ALA 15 (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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116F PHE* 3.6 19.4 - - + -
148F LEU* 5.1 3.8 - - + -
11H ALA 2.9 14.9 + - - +
12H ILE* 3.1 9.2 + - - +
14H GLN* 1.3 74.2 - - - +
16H LEU* 1.3 62.6 + - - +
18H HIS 3.3 1.6 + - - -
19H TYR 3.1 3.5 + - - -
20H ALA* 3.0 28.4 + - - +
23H ASP* 3.6 23.8 - - - +
24H ALA* 3.8 15.0 - - + -
27H LEU* 6.1 1.8 - - + -
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Residues in contact with LEU 16 (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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50F ARG* 5.1 0.3 + - - -
12H ILE 2.8 17.0 + - - +
13H TRP* 3.5 29.4 - - + +
15H ALA* 1.3 75.5 - - - +
17H ASN* 1.3 66.0 + - - +
19H TYR* 3.0 22.5 + - - -
21H TYR* 4.0 25.5 + - + -
24H ALA* 3.8 9.9 - - + -
43H LEU* 4.6 5.2 - - + -
46H THR* 3.7 28.3 - - + -
47H CYS* 3.5 37.9 - - - -
50H ARG* 3.8 23.0 + - + +
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Residues in contact with ASN 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F TRP* 4.8 13.0 - - + -
17F ASN* 5.8 0.2 - - - +
50F ARG* 3.7 20.6 + - - +
13H TRP* 3.0 27.3 + - - +
14H GLN* 3.2 11.4 + - - +
16H LEU* 1.3 80.5 - - - +
18H HIS* 1.3 71.4 + - + +
19H TYR* 3.1 24.2 + - - -
50H ARG* 4.6 4.7 + - - -
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Residues in contact with HIS 18 (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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70F GLN* 5.9 5.3 - - - +
73F TYR* 2.7 59.9 + + + +
77F LYS* 4.2 0.7 - - - +
112F ASP* 5.3 2.5 - - - -
113F SER* 3.3 30.6 - - - -
116F PHE* 3.5 35.0 - + + -
14H GLN* 3.0 27.6 + - + +
15H ALA 3.3 0.6 + - - +
16H LEU 3.2 0.2 - - - -
17H ASN* 1.3 84.7 - - + +
19H TYR* 1.3 73.5 + - - +
20H ALA* 3.2 4.4 + - - -
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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
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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