Contacts of the helix formed by residues 39 - 53 (chain C) in PDB entry 2C2V
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 PRO 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN* 5.3 2.7 - - - +
38B TYR* 3.3 39.9 - - + -
59B GLU* 5.5 0.2 - - - +
61B PHE* 3.2 33.7 - - + -
37C LYS* 3.7 4.2 - - + +
38C VAL* 1.4 88.6 - - + +
40C ARG* 1.3 55.4 + - - +
41C ASN* 3.6 1.8 - - + +
42C PHE* 3.2 20.3 + - + -
43C ARG* 2.8 34.8 + - - +
103C PRO* 5.3 0.2 - - - -
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Residues in contact with ARG 40 (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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39C PRO* 1.3 71.4 - - - +
41C ASN* 1.3 80.0 + - - +
43C ARG* 2.8 5.7 + - - +
44C LEU* 2.5 52.3 + - + +
71C THR* 3.0 30.7 + - - +
72C LEU* 3.7 7.5 + - - +
73C THR* 3.6 15.6 + - - +
98C CYS* 3.1 23.8 + - - +
99C GLY 3.3 18.4 + - - -
100C PRO* 3.7 25.1 - - - +
102C TYR* 3.3 24.1 - - + +
103C PRO* 4.4 5.4 - - - -
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Residues in contact with ASN 41 (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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38B TYR* 4.8 1.4 + - + -
59B GLU* 3.1 41.2 + - - +
74B ARG* 3.6 18.4 - - - +
76B MET* 4.1 7.5 - - - -
39C PRO* 5.7 0.9 - - + -
40C ARG* 1.3 108.2 + - - +
42C PHE* 1.4 62.1 + - + +
44C LEU* 3.1 3.9 + - - +
45C LEU* 2.8 32.7 + - - +
70C MET 5.6 1.1 - - - +
71C THR 5.5 0.3 - - - -
72C LEU* 3.9 11.5 - - - +
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Residues in contact with PHE 42 (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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38B TYR* 4.3 2.5 - + - -
59B GLU* 3.0 53.4 - - + -
61B PHE* 3.8 22.7 - + + -
72B LYS* 3.8 40.8 - - + -
73B VAL 3.8 2.9 - - - -
74B ARG* 3.8 22.9 - - + -
38C VAL* 4.7 7.0 - - + -
39C PRO* 3.2 24.8 + - + +
40C ARG 3.2 1.0 - - - -
41C ASN* 1.4 80.2 - - + +
43C ARG* 1.3 68.0 + - - +
45C LEU* 3.2 16.4 + - + +
46C GLU* 2.8 32.4 + - + +
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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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38C VAL* 4.4 23.4 - - + +
39C PRO 2.8 19.2 + - - +
40C ARG* 2.8 6.2 + - - +
42C PHE* 1.3 80.4 - - - +
44C LEU* 1.4 55.3 + - - +
46C GLU* 2.7 38.9 + - - +
47C GLU* 3.2 25.8 + - - +
102C TYR* 4.4 10.5 - - + -
103C PRO* 3.7 23.6 - - + +
140C ASN* 2.8 24.5 + - - +
141C SER* 4.0 6.5 + - - +
142C TYR 2.8 29.3 + - - -
143C SER* 4.8 2.4 - - - -
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Residues in contact with LEU 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 ARG* 2.5 56.6 + - + +
43C ARG* 1.4 66.3 - - - +
45C LEU* 1.4 58.7 + - - +
46C GLU 2.8 1.1 - - - -
47C GLU* 2.5 34.9 + - - +
48C LEU* 2.8 12.3 + - - +
72C LEU* 3.5 26.9 - - + +
75C TRP* 3.7 30.4 - - + +
98C CYS* 4.4 7.4 - - + -
102C TYR* 3.7 38.8 - - + -
144C ILE* 4.9 1.1 - - + -
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Residues in contact with LEU 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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74B ARG* 4.0 28.7 - - + +
87B LEU* 4.8 6.3 - - + -
89B ARG* 4.0 30.1 - - + +
41C ASN 2.8 18.5 + - - +
42C PHE* 3.7 18.2 - - + +
43C ARG 3.2 0.2 - - - -
44C LEU* 1.4 75.3 - - - +
46C GLU* 1.3 70.3 + - + +
47C GLU 3.1 0.2 + - - -
48C LEU* 3.2 26.6 + - + +
49C GLU* 2.9 30.6 - - - +
72C LEU* 4.1 22.2 - - + -
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Residues in contact with GLU 46 (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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72B LYS* 5.8 6.0 - - - +
38C VAL* 3.1 31.9 - - - +
42C PHE* 2.8 17.7 - - + +
43C ARG* 2.7 20.1 + - - +
45C LEU* 1.3 88.6 - - + +
47C GLU* 1.3 56.1 + - + +
48C LEU 2.9 0.4 - - - -
49C GLU* 3.0 18.0 + - - +
50C GLU* 3.1 14.8 + - - +
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Residues in contact with GLU 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* 3.6 22.3 + - - +
44C LEU* 2.5 14.2 + - + +
46C GLU* 1.3 69.5 - - + +
48C LEU* 1.3 62.2 + - - +
49C GLU 3.0 1.3 - - - -
50C GLU* 4.4 11.9 - - - +
51C GLY* 2.7 27.2 + - - -
62C TRP* 2.7 26.3 + - + +
75C TRP* 4.2 7.4 - - + -
102C TYR* 2.6 39.0 + - - -
143C SER* 2.8 32.0 - - - -
144C ILE* 3.1 24.8 + - + +
145C LYS* 3.7 4.3 + - - +
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Residues in contact with LEU 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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87B LEU* 3.6 29.8 - - + -
89B ARG* 3.8 21.1 - - - +
44C LEU 2.8 10.4 + - - +
45C LEU* 3.3 25.4 - - + +
47C GLU* 1.3 83.4 - - - +
49C GLU* 1.3 57.8 + - + +
51C GLY* 3.4 0.5 - - - -
52C GLN* 2.9 39.8 + - + +
62C TRP 5.3 0.9 - - - +
63C GLY* 5.0 3.1 - - - -
64C LEU* 4.4 20.9 - - + +
72C LEU* 5.9 0.4 - - + -
75C TRP* 3.8 24.1 - - + -
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Residues in contact with GLU 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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89B ARG* 3.3 35.5 + - - +
45C LEU* 2.9 23.8 - - - +
46C GLU* 3.0 5.8 + - - +
48C LEU* 1.3 74.4 - - + +
50C GLU* 1.3 71.8 + - - +
51C GLY 2.6 1.3 - - - -
52C GLN* 3.1 16.3 + - - +
53C LYS* 2.7 45.3 + - + +
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Residues in contact with GLU 50 (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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46C GLU 3.1 12.6 + - - +
47C GLU* 4.0 11.3 - - - +
49C GLU* 1.3 83.3 - - - +
51C GLY* 1.3 68.1 + - - +
53C LYS* 2.9 22.4 + - + +
54C GLY 3.9 6.8 + - - +
55C VAL 4.8 1.1 + - - +
62C TRP* 4.0 13.8 - - + -
145C LYS* 3.0 42.1 + - - +
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Residues in contact with GLY 51 (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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47C GLU 2.7 21.7 + - - -
48C LEU 3.4 1.1 - - - -
49C GLU 2.6 2.0 - - - -
50C GLU* 1.3 82.6 - - - +
52C GLN* 1.3 61.0 + - - -
54C GLY 3.9 8.0 - - - +
55C VAL* 4.9 5.5 - - - +
61C SER* 5.9 0.5 - - - -
62C TRP* 3.2 39.8 + - - +
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Residues in contact with GLN 52 (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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89B ARG* 4.9 6.4 + - - +
48C LEU* 2.9 32.9 + - + +
49C GLU* 3.3 19.8 - - - +
51C GLY* 1.3 77.0 - - - +
53C LYS* 1.4 77.6 + - + +
62C TRP 4.6 1.1 + - - -
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Residues in contact with LYS 53 (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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49C GLU* 2.7 47.4 + - + +
50C GLU* 2.9 9.8 + - + +
52C GLN* 1.4 89.1 + - + +
54C GLY* 1.4 75.4 - - - +
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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