Contacts of the helix formed by residues 41 - 49 (chain C) 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 THR 41 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TYR* 3.4 31.6 - - + +
25C TYR* 3.3 23.3 - - + -
29C CYS* 3.1 11.9 - - - -
39C ASP* 2.8 22.6 + - - -
40C ALA* 1.3 78.1 - - - +
42C ASP* 1.3 54.4 + - - +
44C CYS* 2.9 32.0 + - - +
106C LEU* 4.2 6.5 - - + +
109C ASN* 3.5 22.3 + - + +
110C VAL* 6.3 0.2 - - + -
112C THR* 4.7 0.2 + - - -
113C TYR* 3.8 14.1 - - + -
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.5 0.8 - - + +
26C GLY* 3.3 12.9 - - - -
27C CYS* 2.5 30.2 + - - +
28C TYR* 2.4 25.5 + - - +
29C CYS* 3.0 16.7 + - - -
37C PRO* 2.9 19.6 - - - +
38C GLN* 2.8 26.7 + - + +
39C ASP* 2.4 29.8 + - - +
41C THR* 1.3 72.2 - - - +
43C ARG* 1.3 56.9 + - - +
44C CYS 3.2 1.3 - - - -
45C CYS 4.2 1.1 - - - -
46C PHE* 3.6 11.4 + - - +
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C PRO* 3.2 26.9 - - + +
39C ASP 2.6 16.7 + - - +
40C ALA* 2.9 11.6 + - - +
42C ASP* 1.3 72.1 - - - +
44C CYS* 1.3 61.3 + - - +
45C CYS 3.4 0.2 - - - -
46C PHE* 4.0 7.3 - - + -
47C VAL* 2.9 48.7 + - - +
105C CYS* 4.9 1.0 - - - -
131C GLU* 3.4 28.6 + - - -
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Residues in contact with CYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 2.9 16.5 + - - -
41C THR* 2.9 16.4 + - - +
43C ARG* 1.3 81.4 - - - +
45C CYS* 1.3 60.4 + - - +
47C VAL* 3.6 5.1 + - - +
48C HIS* 3.5 18.0 + - - +
102C ALA* 5.1 7.1 - - - +
105C CYS* 2.0 66.7 - - + +
106C LEU* 3.4 20.2 - - + -
109C ASN* 3.6 8.3 - - - -
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Residues in contact with CYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 6.5 0.9 - - - -
22C TYR* 5.0 6.3 - - - -
28C TYR 2.9 24.7 - - - +
29C CYS* 2.0 48.4 - - - -
41C THR 3.4 3.3 + - - -
44C CYS* 1.3 75.5 - - - +
46C PHE* 1.3 53.5 + - - +
48C HIS* 3.1 10.0 - - - +
49C ASP* 2.8 38.3 + - - +
102C ALA* 6.3 0.4 - - - -
106C LEU* 4.2 17.0 - - - -
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Residues in contact with PHE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 3.5 41.9 - + + +
37C PRO* 3.3 31.9 - - + -
42C ASP 3.6 7.2 + - - +
43C ARG* 4.2 9.9 - - + +
44C CYS 3.4 0.6 - - - -
45C CYS* 1.3 74.9 - - - +
47C VAL* 1.3 80.2 + - + +
49C ASP* 2.9 18.4 + - + +
50C CYS* 3.2 7.2 + - + +
131C GLU* 3.2 40.8 - - + -
132C GLN 3.4 24.2 - - - -
133C CYS* 3.5 22.0 - - - -
70D LEU* 5.2 2.9 - - + -
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 2.9 38.1 - - - +
44C CYS* 3.7 7.4 - - - +
46C PHE* 1.3 83.1 - - + +
48C HIS* 1.3 53.3 + - - +
50C CYS* 2.5 30.6 + - - +
51C CYS* 2.7 24.4 + - + -
101C ALA* 6.2 3.8 - - + -
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Residues in contact with HIS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PHE* 5.6 0.2 - + - -
5C PHE* 3.2 31.5 - + - -
44C CYS 3.5 9.3 + - - +
45C CYS* 3.1 16.4 + - - +
47C VAL* 1.3 79.5 - - - +
49C ASP* 1.3 59.9 + - - +
50C CYS 2.9 3.5 + - - -
51C CYS* 3.8 9.4 - - - +
52C TYR* 3.1 67.1 + + - +
98C CYS* 3.7 11.4 - - + -
99C ASP* 3.2 18.3 + - - -
102C ALA* 3.2 29.8 - - + -
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Residues in contact with ASP 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 3.3 36.0 - - + +
33C GLY* 4.9 0.9 - - - -
45C CYS* 2.8 19.5 + - - +
46C PHE* 2.9 13.6 + - - +
48C HIS* 1.3 79.8 + - - +
50C CYS* 1.3 57.7 + - - +
51C CYS 3.8 0.2 - - - -
52C TYR* 4.6 6.1 - - - +
53C GLY 4.4 5.9 + - - -
61D ASN* 4.7 3.5 - - - +
69D LYS* 4.0 34.3 + - + +
70D LEU* 2.9 37.2 - - + +
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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