Contacts of the helix formed by residues 49 - 63 (chain C) in PDB entry 1V14
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 SER 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C ARG 4.1 9.4 - - - -
6C ASN* 4.2 12.3 - - - +
47C PHE* 3.3 4.9 - - - +
48C LYS* 1.3 80.9 - - - +
50C PHE* 1.3 63.5 + - - +
51C ASP* 3.0 31.5 + - - +
52C ASP* 3.0 18.8 + - - +
53C PHE 3.2 8.1 + - - -
114C TYR* 3.4 11.4 - - - -
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Residues in contact with PHE 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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5C ARG* 3.1 62.4 + - + +
49C SER* 1.3 73.8 - - - +
51C ASP* 1.3 58.4 + - - +
53C PHE* 3.0 29.9 + + + +
54C ARG* 3.0 35.3 + - + +
101C LEU* 4.2 26.9 - - + -
113C VAL* 3.9 26.9 - - + -
114C TYR* 3.3 13.1 + + - -
119C ILE* 3.9 18.8 - - + -
7I G 3.4 21.8 - - - -
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Residues in contact with ASP 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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5C ARG* 4.9 4.7 + - - +
6C ASN* 3.7 16.8 - - - +
49C SER* 3.0 17.6 + - - +
50C PHE* 1.3 79.2 - - - +
52C ASP* 1.3 58.3 + - - +
54C ARG* 3.0 40.6 + - - +
55C LYS* 3.4 20.4 + - - +
7I G 4.3 3.1 - - - +
8I C 3.0 29.1 + - + +
9J G 5.2 0.5 - - - +
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Residues in contact with ASP 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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46C GLU 5.0 0.7 - - - +
47C PHE* 3.4 21.7 - - + -
48C LYS* 4.3 13.0 + - + +
49C SER* 3.0 19.0 + - - +
51C ASP* 1.3 77.6 - - - +
53C PHE* 1.3 64.0 + - - +
54C ARG 3.3 0.4 - - - -
55C LYS* 3.5 14.3 + - - +
56C ALA* 3.1 22.9 + - - +
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Residues in contact with PHE 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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11C ALA* 4.1 19.1 - - + -
34C ILE* 5.5 4.0 - - + -
42C LEU* 4.7 3.6 - - + -
47C PHE* 3.7 31.9 - + + -
49C SER 3.2 5.1 + - - -
50C PHE* 3.0 35.4 + + - +
52C ASP* 1.3 76.0 - - - +
54C ARG* 1.3 60.9 + - - +
56C ALA* 3.1 6.2 + - - +
57C VAL* 2.9 52.9 + - + +
101C LEU* 4.3 7.4 - - + -
114C TYR* 4.0 24.0 - + + -
116C MET* 4.1 22.4 - - + -
119C ILE* 3.5 30.7 - - + -
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Residues in contact with ARG 54 (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 ARG* 3.8 10.1 - - - +
50C PHE* 3.0 15.8 + - + +
51C ASP* 3.0 47.7 + - - +
53C PHE* 1.3 79.5 - - - +
55C LYS* 1.3 66.1 + - - +
57C VAL* 2.9 16.2 + - - +
58C TRP* 3.0 41.1 + - + +
82C GLY 5.3 0.9 - - - -
84C SER* 5.2 0.7 - - - -
101C LEU* 4.1 14.1 - - + -
7I G 2.9 56.7 + - - -
8I C 3.2 41.1 + - - -
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Residues in contact with LYS 55 (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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51C ASP 3.4 12.4 + - - +
52C ASP* 3.7 18.2 - - - +
53C PHE 3.4 0.2 - - - -
54C ARG* 1.3 78.1 - - - +
56C ALA* 1.3 58.3 + - - +
58C TRP 3.3 0.5 + - - -
59C GLU* 3.0 50.8 + - - +
81C LYS* 2.8 27.5 + - - +
82C GLY* 3.4 23.0 - - - +
83C TYR* 5.4 8.5 + - + -
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Residues in contact with ALA 56 (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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42C LEU* 3.8 12.1 - - + +
47C PHE* 3.6 25.1 - - + -
52C ASP* 3.1 16.5 + - - +
53C PHE 3.6 7.4 - - - +
55C LYS* 1.3 73.6 - - - +
57C VAL* 1.3 64.0 + - - +
59C GLU* 3.9 10.2 - - - +
60C GLU* 3.3 30.0 + - - +
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Residues in contact with VAL 57 (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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22C TRP* 6.5 0.4 - - + -
34C ILE* 4.6 13.7 - - + -
35C PRO* 6.4 0.4 - - + -
38C ILE* 4.0 19.8 - - + +
42C LEU* 3.9 15.5 - - + -
53C PHE* 2.9 53.6 + - + +
54C ARG* 2.9 9.6 + - - +
56C ALA* 1.3 78.4 - - - +
58C TRP* 1.3 71.4 + - + +
60C GLU* 3.6 0.4 + - - -
61C VAL* 3.0 29.6 + - + +
101C LEU* 4.6 13.7 - - + -
116C MET* 6.0 0.4 - - - -
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Residues in contact with TRP 58 (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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22C TRP* 4.8 15.0 - + - -
23C LEU* 5.3 3.8 - - + -
54C ARG* 3.0 44.4 + - + +
57C VAL* 1.3 79.1 - - + +
59C GLU* 1.3 67.2 + - - +
61C VAL* 3.4 18.4 - - + +
62C SER 3.3 5.5 + - - -
71C LEU* 6.3 0.2 - - + -
79C VAL* 3.0 41.2 - - + +
82C GLY 3.8 25.4 - - - +
83C TYR 4.2 0.2 - - - +
84C SER* 3.6 33.5 - - - -
85C PRO* 3.5 29.8 - - + -
99C TYR* 4.0 22.6 + + + -
101C LEU* 4.1 25.1 - - + +
121C VAL* 4.4 12.6 - - + -
7I G 5.1 0.2 + - - -
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Residues in contact with GLU 59 (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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55C LYS* 3.0 52.0 + - - +
56C ALA* 3.9 8.7 - - - +
57C VAL 3.3 0.4 - - - -
58C TRP* 1.3 76.3 - - - +
60C GLU* 1.3 58.7 + - + +
62C SER* 2.4 31.9 + - - +
63C LYS* 3.2 18.1 + - - +
79C VAL 3.2 14.1 - - - +
80C SER 3.9 13.7 - - - +
81C LYS 4.1 0.9 - - - +
82C GLY* 3.8 5.6 - - - -
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Residues in contact with GLU 60 (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 ILE* 3.5 24.2 - - + +
41C LYS* 2.7 59.3 + - + +
42C LEU* 4.0 15.2 - - + +
45C LYS* 4.6 7.6 + - - -
56C ALA* 3.3 19.3 + - + +
57C VAL* 4.1 1.3 - - - +
58C TRP 3.4 0.2 - - - -
59C GLU* 1.3 76.3 - - + +
61C VAL* 1.3 59.7 + - - +
62C SER 3.4 0.2 - - - -
63C LYS* 3.4 24.7 + - - +
64C ASP* 3.4 17.7 + - - +
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Residues in contact with VAL 61 (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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22C TRP* 4.6 17.0 - - + -
38C ILE* 3.8 17.0 - - + -
57C VAL* 3.0 22.2 - - + +
58C TRP* 3.4 28.7 - - + +
59C GLU 3.0 0.6 - - - -
60C GLU* 1.3 76.6 - - - +
62C SER* 1.3 61.3 + - - +
63C LYS 3.1 0.2 - - - -
64C ASP* 2.9 27.0 + - - +
67C LEU* 4.0 29.8 - - + +
68C SER* 3.9 8.5 - - - +
71C LEU* 5.0 4.9 - - + -
79C VAL* 4.5 10.1 - - + -
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Residues in contact with SER 62 (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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58C TRP 3.3 2.2 + - - -
59C GLU* 2.4 26.8 + - - +
61C VAL* 1.3 78.9 - - - +
63C LYS* 1.3 62.5 + - - +
64C ASP 3.3 4.0 + - - -
65C PRO* 5.0 0.5 - - - +
68C SER* 4.2 11.1 + - - -
76C LYS* 4.6 4.0 - - - +
79C VAL* 3.6 30.9 + - - +
80C SER* 3.7 25.0 + - - -
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Residues in contact with LYS 63 (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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41C LYS* 5.0 4.9 - - - +
59C GLU* 3.2 25.1 + - - +
60C GLU* 3.7 29.2 - - - +
61C VAL 3.1 0.8 - - - -
62C SER* 1.3 80.3 - - - +
64C ASP* 1.3 56.8 + - - +
65C PRO* 3.4 10.2 - - - +
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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