Contacts of the helix formed by residues 39 - 55 (chain F) 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 ASP 39 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F TYR* 2.3 45.9 + - - -
37F PRO* 4.6 0.9 - - - +
38F LYS* 1.3 76.8 + - - +
40F ALA* 1.3 68.9 + - - +
41F THR* 3.6 4.0 + - - -
42F ASP* 3.1 10.5 + - - +
43F ARG* 3.1 20.0 + - - +
112F THR* 4.2 15.4 - - - +
114F ASP* 4.4 0.9 + - - +
117F TYR* 2.7 23.9 - - + -
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Residues in contact with ALA 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASP* 1.3 75.3 - - - +
41F THR* 1.3 65.8 + - - +
43F ARG* 2.8 26.3 + - - +
44F CYS* 3.3 9.8 + - - -
105F CYS* 4.9 0.3 - - - -
109F ASN* 3.4 31.1 + - - +
112F THR* 3.6 17.7 - - + +
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Residues in contact with THR 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TYR* 3.9 17.9 - - + -
25F TYR* 3.8 24.2 - - + -
29F CYS* 4.4 0.9 - - - -
39F ASP* 3.6 8.5 + - - -
40F ALA* 1.3 75.1 - - - +
42F ASP* 1.3 56.0 + - - +
44F CYS* 2.8 39.6 + - - +
45F CYS 3.6 2.4 + - - -
106F PHE* 3.7 23.7 - - + -
109F ASN* 3.7 15.5 + - - +
110F MET* 5.4 0.3 - - - -
112F THR* 3.4 15.1 + - - -
113F TYR* 4.2 13.2 + - + -
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Residues in contact with ASP 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F TYR* 2.7 30.3 - - + +
26F GLY* 4.1 2.9 - - - -
27F CYS* 3.4 14.8 + - - +
28F TYR* 3.0 24.8 + - - +
29F CYS* 3.8 10.3 + - - -
37F PRO* 3.4 8.6 - - - +
38F LYS* 2.8 30.5 + - + +
39F ASP* 3.1 19.7 + - - +
41F THR* 1.3 80.0 - - - +
43F ARG* 1.3 60.4 + - - +
45F CYS* 3.3 13.0 + - - +
46F PHE* 3.5 7.3 + - - +
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Residues in contact with ARG 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PRO* 3.9 25.8 - - + +
39F ASP 3.1 12.5 + - - +
40F ALA* 2.8 18.9 + - - +
42F ASP* 1.3 75.0 - - - +
44F CYS* 1.3 62.8 + - - -
46F PHE* 3.0 9.1 + - + +
47F VAL* 3.0 57.0 + - + +
105F CYS* 4.6 14.5 - - - -
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Residues in contact with CYS 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F ALA 3.4 9.4 - - - -
41F THR* 2.8 22.1 + - - +
43F ARG* 1.3 72.5 - - - +
45F CYS* 1.3 53.2 + - - +
46F PHE 2.9 5.2 - - - -
47F VAL* 3.2 7.9 + - - +
48F HIS* 2.6 37.5 + - - +
102F ALA* 4.3 9.8 - - - +
105F CYS* 2.6 61.2 - - + -
106F PHE* 4.1 13.9 - - + -
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Residues in contact with CYS 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 6.0 2.0 - - - -
22F TYR* 4.9 0.9 - - - -
28F TYR* 3.3 5.2 - - - +
29F CYS* 2.0 65.1 - - - +
42F ASP 3.3 3.5 + - - +
43F ARG 3.2 0.6 - - - -
44F CYS* 1.3 77.3 - - - +
46F PHE* 1.3 51.8 + - - +
48F HIS* 3.8 13.7 - - - +
49F ASP* 2.5 35.7 - - - +
106F PHE* 2.9 31.9 - - - -
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Residues in contact with PHE 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E MET* 4.3 6.5 - - - -
28F TYR* 3.2 46.0 - + + -
37F PRO* 3.8 21.1 - - + -
42F ASP 3.5 1.7 + - - +
43F ARG* 3.0 18.4 + - + +
44F CYS 2.9 0.4 - - - -
45F CYS* 1.3 80.5 - - - +
47F VAL* 1.3 60.3 + - + +
48F HIS 3.2 1.1 - - - -
49F ASP* 3.4 0.7 + - - +
50F CYS* 2.8 61.2 + - - -
131F ASP* 2.7 41.3 - - + -
132F GLN 3.3 14.1 - - - -
133F CYS* 3.9 5.6 - - - -
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ARG* 3.0 52.6 + - + +
44F CYS* 3.6 7.4 - - - +
46F PHE* 1.3 79.3 - - + +
48F HIS* 1.3 59.1 + - - +
50F CYS* 3.5 8.0 - - + +
51F CYS* 2.8 34.5 + - + +
54F ARG* 5.4 7.4 - - - +
101F VAL* 5.9 7.2 - - + -
102F ALA* 6.3 0.2 - - + -
105F CYS* 6.0 0.7 - - - -
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Residues in contact with HIS 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 4.2 7.6 + - - -
2F LEU* 5.2 3.4 - - + -
5F PHE* 3.2 40.4 - + + -
44F CYS 2.6 22.5 + - - +
45F CYS* 3.8 10.9 + - - +
47F VAL* 1.3 74.0 - - - +
49F ASP* 1.3 76.1 + - - +
51F CYS* 3.4 6.8 - - - +
52F TYR* 2.9 48.9 + + - +
98F CYS 3.8 8.5 - - - -
99F ASP* 2.7 28.9 + - - -
102F ALA* 3.7 19.0 - - + +
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Residues in contact with ASP 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 2.7 47.7 + - + +
70E MET* 3.8 18.4 - - + +
28F TYR* 3.6 24.5 - - - +
33F GLY* 5.4 0.7 + - - -
45F CYS* 2.5 25.8 + - - +
46F PHE 3.4 4.1 + - - +
47F VAL 3.3 0.2 - - - -
48F HIS* 1.3 80.0 + - - +
50F CYS* 1.3 69.4 + - - +
52F TYR* 2.7 12.7 + - - +
53F ALA* 2.7 23.8 + - - +
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Residues in contact with CYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PHE* 2.8 48.1 + - - +
47F VAL* 3.5 9.0 - - + +
49F ASP* 1.3 71.9 - - - +
51F CYS* 1.3 63.1 + - - +
53F ALA* 2.8 16.9 + - - +
54F ARG* 3.0 25.1 + - - +
133F CYS* 2.0 64.2 - - + +
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Residues in contact with CYS 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 2.8 23.5 + - + +
48F HIS* 3.4 4.0 - - - +
50F CYS* 1.3 71.2 - - - +
52F TYR* 1.3 63.2 + - - +
54F ARG* 2.9 42.7 + - - +
55F VAL* 3.3 14.6 + - - +
94F ALA* 3.6 5.4 - - - -
97F GLU* 4.7 2.7 - - - -
98F CYS* 2.0 52.7 - - + -
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Residues in contact with TYR 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 4.9 13.9 - - + -
1F ASN 4.1 9.7 + - - -
2F LEU* 4.3 11.7 - - + +
48F HIS* 2.9 33.1 + + - +
49F ASP* 2.7 18.2 + - - +
51F CYS* 1.3 73.2 - - - +
53F ALA* 1.3 57.4 + - - +
55F VAL* 3.6 19.9 + - - +
68F PRO* 3.3 47.3 + - + +
69F LYS* 4.4 2.9 - - + -
95F VAL* 4.2 17.6 - - + +
98F CYS* 3.3 29.2 - - + -
99F ASP* 2.7 41.1 + - - -
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ASN* 3.8 41.2 - - + +
70E MET* 4.8 6.7 - - + -
49F ASP 2.7 13.6 + - - +
50F CYS* 2.8 16.8 + - - +
52F TYR* 1.3 72.8 - - - +
54F ARG* 1.3 60.5 + - + +
55F VAL 3.1 9.6 + - - +
56F LYS* 4.9 5.2 - - - +
133F CYS* 5.4 3.4 - - + -
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Residues in contact with ARG 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 4.7 7.3 + - - +
50F CYS* 3.0 16.5 + - - +
51F CYS* 2.9 43.8 + - - +
53F ALA* 1.3 75.9 - - + +
55F VAL* 1.3 59.2 + - + +
56F LYS* 3.2 20.6 + - - +
133F CYS* 4.4 18.2 + - + +
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Residues in contact with VAL 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F CYS* 3.5 15.0 - - - +
52F TYR* 3.7 15.6 - - - +
53F ALA 3.1 5.7 - - - +
54F ARG* 1.3 74.9 - - + +
56F LYS* 1.3 60.2 + - - +
58F GLY 4.2 0.9 + - - -
59F CYS* 3.3 39.0 - - - +
68F PRO* 5.3 5.5 - - + +
91F CYS* 3.9 13.2 - - + -
94F ALA* 3.3 39.9 - - + +
95F VAL* 4.0 9.4 - - + +
98F CYS* 4.3 4.5 - - - -
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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