Contacts of the helix formed by residues 74 - 82 (chain C) in PDB entry 3VVK
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 VAL 74 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C SER 4.1 1.8 - - - +
71C THR* 3.0 15.6 + - + +
73C LEU* 1.3 75.6 - - - +
75C PRO* 1.4 68.4 - - + +
77C VAL* 3.0 6.6 + - - +
78C SER* 2.8 25.6 + - - -
130C SER* 4.1 12.8 - - - +
133C MET* 4.0 17.0 - - + -
134C ILE* 3.4 33.0 - - + +
256C LYS* 3.4 45.5 - - + +
260C ALA* 5.4 1.6 - - + -
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Residues in contact with PRO 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 3.5 26.9 - - - +
48C SER* 4.0 10.1 - - - -
49C ILE* 3.9 12.4 - - + +
52C PHE* 4.0 25.1 - - + -
71C THR 3.3 6.7 - - - +
72C ILE 3.0 23.6 - - - +
74C VAL* 1.4 91.4 - - + +
76C VAL* 1.3 55.4 + - - +
78C SER* 3.6 9.6 - - - -
79C ILE* 2.9 25.8 + - - +
256C LYS 4.6 2.9 - - - +
257C TYR* 4.1 13.0 - - + -
260C ALA* 5.1 0.2 - - + -
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 4.5 28.3 - - + -
158B ALA* 5.4 7.0 - - + -
182B ILE* 6.2 3.8 - - + -
186B CYS* 5.5 4.5 - - - -
49C ILE* 3.8 24.0 - - + -
72C ILE* 3.1 26.2 - - + +
73C LEU* 3.4 19.3 - - + +
74C VAL 3.0 0.4 - - - -
75C PRO* 1.3 75.3 - - - +
77C VAL* 1.3 67.4 + - + +
79C ILE* 3.2 8.5 - - + +
80C ALA* 3.1 24.0 + - + +
303E L3P 5.3 8.1 - - + -
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Residues in contact with VAL 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 2.8 22.8 + - + +
74C VAL 3.4 7.0 - - - +
76C VAL* 1.3 78.4 - - + +
78C SER* 1.3 56.9 + - - +
80C ALA* 3.4 1.7 + - - +
81C SER* 2.9 29.1 + - - -
125C LEU 4.5 0.9 - - - +
126C THR* 3.6 31.2 - - - +
129C LEU* 3.6 40.8 - - + +
130C SER* 3.7 8.7 - - - +
133C MET* 5.0 2.5 - - + -
303C L3P 5.6 0.3 - - - +
303E L3P 4.3 28.4 - - + +
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Residues in contact with SER 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 4.5 0.9 - - - -
74C VAL 2.8 15.6 + - - -
75C PRO* 3.8 8.7 - - - -
76C VAL 3.2 0.2 - - - -
77C VAL* 1.3 78.6 - - - +
79C ILE* 1.3 57.0 + - - +
82C TYR* 2.9 51.9 + - - -
126C THR* 4.1 10.4 - - - +
256C LYS* 3.9 20.1 - - - +
257C TYR* 2.9 26.8 + - - -
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Residues in contact with ILE 79 (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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178B PHE* 4.8 7.2 - - + -
182B ILE* 4.7 25.8 - - + -
42C ILE* 3.8 37.6 - - + +
45C ALA* 3.7 10.0 - - + +
46C GLY* 4.2 15.5 - - - +
49C ILE* 4.3 9.0 - - + -
75C PRO 2.9 19.5 + - - +
76C VAL* 3.2 18.4 - - + +
78C SER* 1.3 72.4 - - - +
80C ALA* 1.3 66.0 + - + +
82C TYR* 4.2 3.2 - - - +
83C THR* 2.6 37.6 + - - +
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Residues in contact with ALA 80 (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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162B THR* 4.3 24.0 - - + -
179B TRP* 3.2 20.9 - - + -
182B ILE* 4.9 9.6 - - + -
76C VAL* 3.1 14.5 + - + +
77C VAL 3.8 2.9 - - - +
79C ILE* 1.3 85.1 - - + +
81C SER* 1.3 61.3 + - - +
83C THR* 3.4 2.6 + - - -
84C GLY 3.1 14.7 + - - -
303C L3P 3.6 12.7 - - + +
303E L3P 4.8 9.2 - - + -
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 2.9 19.4 + - - -
80C ALA* 1.3 76.0 - - - +
82C TYR* 1.3 58.6 + - - +
84C GLY* 2.7 20.8 + - - -
85C LEU* 3.0 13.8 + - - +
90C THR* 4.4 1.2 + - - -
122C GLY* 3.4 13.5 + - - -
125C LEU* 4.0 5.8 - - - +
126C THR* 2.5 41.9 + - - -
129C LEU* 6.2 0.2 - - - -
303C L3P 3.7 17.1 - - - +
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Residues in contact with TYR 82 (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 SER 4.0 0.9 - - - -
38C LEU* 3.7 33.5 - - + +
41C ASN* 3.4 43.9 + - + -
42C ILE* 3.7 21.7 - - + +
78C SER* 2.9 46.1 + - - +
79C ILE 4.3 0.2 - - - +
81C SER* 1.3 76.5 - - - +
83C THR* 1.3 58.3 + - - +
85C LEU* 3.2 11.6 + - + +
86C ALA* 2.9 31.9 + - - +
123C ARG* 2.8 28.0 + - - -
126C THR* 4.8 9.9 - - + -
249C SER* 3.7 4.3 + - - -
252C ASP* 2.6 31.6 + - - +
257C TYR* 4.5 0.2 - - - -
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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