Contacts of the helix formed by residues 40 - 52 (chain E) in PDB entry 2H4C
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 ALA 40 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E ASP* 1.3 77.8 - - + +
41E THR* 1.3 59.0 + - - +
42E ASP 3.2 0.2 - - - -
43E ARG* 2.9 38.9 + - - +
44E CYS* 3.0 18.1 + - - -
105E CYS* 4.6 1.2 - - - -
109E ASN* 3.5 32.8 - - + +
112E THR* 4.8 10.7 - - + +
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Residues in contact with THR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E TYR* 3.1 41.1 - - + +
25E TYR* 3.7 18.2 + - + -
29E CYS* 4.1 1.1 - - - -
39E ASP* 3.3 11.5 + - - -
40E ALA* 1.3 71.7 - - - +
42E ASP* 1.3 59.5 + - - +
43E ARG 3.0 6.5 + - - -
44E CYS* 3.6 6.2 + - - -
45E CYS* 3.1 26.0 - - - -
106E LEU* 3.5 16.5 - - + +
109E ASN* 3.7 21.7 + - + +
110E VAL* 6.5 0.2 - - - -
112E THR* 5.0 0.2 - - - -
113E TYR* 4.0 13.7 - - + -
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E TYR* 3.9 4.9 - - + -
26E GLY* 2.7 14.2 - - - -
27E CYS 2.6 26.4 + - - -
28E TYR* 3.3 28.2 + - - +
29E CYS* 4.2 7.4 - - - -
37E PRO* 3.9 6.3 - - + +
38E GLN* 2.8 26.7 + - - +
39E ASP* 3.5 22.1 + - - +
40E ALA 3.2 0.2 - - - -
41E THR* 1.3 78.1 - - - +
43E ARG* 1.3 57.7 + - - +
45E CYS* 4.0 2.5 - - - +
46E PHE* 3.4 20.3 + - - +
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Residues in contact with ARG 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PRO* 4.4 18.9 + - + +
38E GLN 4.7 7.5 + - - -
39E ASP* 3.0 27.5 + - - +
40E ALA* 2.9 25.9 + - - +
42E ASP* 1.3 79.0 - - - +
44E CYS* 1.3 68.0 + - - +
45E CYS 2.9 2.0 + - - -
46E PHE* 2.9 14.0 + - - +
47E VAL* 3.1 20.5 + - + +
105E CYS* 5.8 0.4 - - - -
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Residues in contact with CYS 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ALA 3.0 16.3 + - - -
41E THR* 3.6 1.5 + - - -
43E ARG* 1.3 77.9 - - - +
45E CYS* 1.3 60.6 + - - +
47E VAL* 3.5 6.4 + - - +
48E HIS* 3.2 21.7 + - - +
102E ALA* 4.6 10.5 - - + +
105E CYS* 2.0 51.7 - - + -
106E LEU* 2.9 49.4 - - + -
109E ASN* 4.3 2.7 - - - -
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Residues in contact with CYS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E PHE* 6.5 1.3 - - - -
22E TYR* 5.2 0.4 - - - -
28E TYR* 3.7 5.8 - - + -
29E CYS* 2.0 68.0 - - - +
41E THR 3.1 8.7 - - - +
42E ASP 4.0 2.2 - - - +
43E ARG 2.9 1.0 - - - -
44E CYS* 1.3 80.2 - - - +
46E PHE* 1.3 58.8 + - - +
48E HIS* 3.5 6.4 + - - +
49E ASP* 2.7 33.1 + - - +
106E LEU* 4.1 17.0 - - - -
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Residues in contact with PHE 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E TYR* 3.2 49.7 - + + +
37E PRO* 5.2 9.6 - - + -
42E ASP 3.4 15.1 + - - +
43E ARG* 2.9 8.2 + - - +
45E CYS* 1.3 77.5 - - - +
47E VAL* 1.3 65.4 + - + +
49E ASP* 3.4 4.2 + - - +
50E CYS* 3.1 42.3 + - - -
131E GLU* 3.1 49.8 - - + -
132E GLN* 3.8 22.0 - - - -
133E CYS* 4.2 2.5 - - + -
70F LEU* 4.1 13.0 - - + -
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ARG* 3.1 15.1 + - + +
44E CYS* 3.8 9.2 - - - +
46E PHE* 1.3 80.5 - - + +
48E HIS* 1.3 53.0 + - - +
50E CYS* 2.7 13.1 + - + +
51E CYS* 2.5 40.6 + - + +
101E ALA* 6.1 4.9 - - + -
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Residues in contact with HIS 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.4 38.0 - + + -
44E CYS 3.2 14.6 + - - +
45E CYS* 3.7 12.3 - - - +
46E PHE 3.3 0.4 - - - -
47E VAL* 1.3 77.1 - - - +
49E ASP* 1.3 56.9 + - - +
51E CYS* 3.6 3.9 - - + +
52E TYR* 2.7 56.9 + + - +
98E CYS* 3.4 28.7 - - + +
99E ASP* 2.9 41.4 + - - -
102E ALA* 3.7 12.3 - - + +
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Residues in contact with ASP 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E TYR* 4.0 12.5 - - + +
29E CYS 5.3 0.3 - - - +
45E CYS* 2.7 22.2 - - - +
46E PHE* 3.4 10.7 + - - +
47E VAL 3.1 0.4 - - - -
48E HIS* 1.3 78.7 + - - +
50E CYS* 1.3 60.6 + - - +
52E TYR* 4.0 13.2 - - - +
53E GLY 3.8 2.3 + - - -
61F ASN* 3.7 21.8 + - - -
69F LYS* 3.1 35.4 + - - +
70F LEU* 3.5 32.9 - - + +
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Residues in contact with CYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PHE* 3.1 36.9 + - - -
47E VAL* 2.7 17.0 + - + +
49E ASP* 1.3 80.6 - - - +
51E CYS* 1.3 58.5 + - - +
52E TYR 3.1 0.9 - - - -
53E GLY* 2.9 16.4 + - - -
54E THR* 3.2 19.0 + - - +
133E CYS* 2.0 55.0 - - + -
70F LEU* 6.3 0.9 - - - -
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Residues in contact with CYS 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 2.5 25.2 + - + +
48E HIS* 3.6 7.4 - - - +
50E CYS* 1.3 73.8 - - - +
52E TYR* 1.3 55.3 + - - +
53E GLY 3.3 1.7 + - - -
54E THR* 3.2 21.2 + - - -
55E VAL* 3.3 12.0 - - - +
94E THR* 4.6 3.3 - - - +
97E GLU 5.1 0.4 - - - -
98E CYS* 2.0 56.3 - - + -
101E ALA* 6.3 0.7 - - - -
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Residues in contact with TYR 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN 4.4 10.2 + - - -
2E PHE* 4.9 12.7 - + - -
5E PHE* 4.8 3.1 - - - +
48E HIS* 2.7 39.6 + + - +
49E ASP* 4.1 13.7 - - - +
51E CYS* 1.3 74.4 - - - +
53E GLY* 1.3 59.2 + - - +
55E VAL* 3.8 15.5 - - + +
68E PRO* 3.3 39.2 + - + +
69E LYS* 4.2 9.9 - - + -
95E VAL* 4.1 17.9 - - + +
98E CYS* 3.9 16.4 - - + -
99E ASP* 3.1 30.3 + - - -
61F ASN* 4.4 5.0 + - - +
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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