Contacts of the helix formed by residues 70 - 84 (chain C) in PDB entry 3V5I
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 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 2.7 14.6 + - - +
37C ASP* 4.5 6.1 - - - -
38C ASP* 4.5 3.8 + - - -
69C GLY* 1.3 70.8 - - - -
71C VAL* 1.3 58.2 + - - +
72C THR* 3.4 10.0 + - - -
73C ALA* 3.1 31.1 + - - +
74C GLY* 2.9 25.5 + - - -
99C MET* 4.0 2.9 - - - +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY 3.3 4.9 + - - +
70C SER* 1.3 71.9 + - - +
72C THR* 1.3 63.0 + - + +
74C GLY* 3.1 2.8 + - - -
75C PHE* 2.9 52.7 + - + -
99C MET* 3.6 29.6 - - + +
125C PRO* 4.4 16.4 - - + -
126C LEU 6.1 0.9 - - - +
146C THR* 3.8 22.2 - - + -
150C LEU* 4.3 10.5 - - + -
119D GLU* 6.1 0.4 - - - +
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Residues in contact with THR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 4.7 5.0 + - - -
70C SER* 3.4 7.0 + - - -
71C VAL* 1.3 77.6 - - + +
73C ALA* 1.3 68.3 + - - +
75C PHE* 3.1 9.9 + - + +
76C ALA 3.0 18.4 + - - -
142C HIS* 6.0 1.3 - - + -
65D ASN* 4.9 1.6 + - - -
94D GLY* 3.4 18.9 - - - +
95D MET* 3.9 35.9 - - + +
119D GLU* 3.9 24.9 - - - +
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Residues in contact with ALA 73 (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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36C ILE* 3.9 7.4 - - + -
37C ASP 3.6 22.0 - - - +
38C ASP* 3.6 20.0 - - - +
41C ALA* 3.4 23.3 - - + +
70C SER* 3.1 26.9 + - - +
72C THR* 1.3 77.6 + - - +
74C GLY* 1.3 62.6 + - - +
76C ALA* 3.3 10.6 + - - +
77C ILE* 3.4 6.6 + - - +
65D ASN* 4.6 2.2 - - - +
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Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.8 8.9 - - - +
70C SER 2.9 16.0 + - - -
71C VAL 3.5 4.7 - - - -
73C ALA* 1.3 77.0 - - - +
75C PHE* 1.3 56.5 + - - +
77C ILE* 3.1 9.3 + - - +
78C TYR* 2.8 24.6 + - - +
99C MET* 3.7 21.3 - - - -
103C LEU* 3.6 12.9 - - - +
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Residues in contact with PHE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 2.9 40.8 + - + -
72C THR* 3.1 12.5 + - + +
74C GLY* 1.3 74.3 - - - +
76C ALA* 1.3 59.7 + - - +
78C TYR* 4.0 14.4 - + + -
79C ASP* 2.8 34.6 + - - +
99C MET* 5.2 1.3 - - - -
102C PHE* 3.7 23.1 - + - -
146C THR* 5.2 0.9 - - + -
149C LYS* 3.5 36.8 - - + -
150C LEU* 3.6 26.2 - - + -
153C ILE* 3.8 15.9 - - + -
94D GLY* 4.7 5.4 - - - +
117D ASN* 3.7 31.2 - - + +
119D GLU* 5.9 0.7 - - - -
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA* 4.5 3.8 - - + -
45C VAL* 3.9 10.3 - - + -
72C THR 3.0 7.0 + - - +
73C ALA 3.4 10.5 - - - +
75C PHE* 1.3 77.3 - - - +
77C ILE* 1.3 60.4 + - - +
79C ASP* 4.1 2.0 - - - +
80C THR* 2.8 30.5 + - - -
65D ASN* 4.2 13.0 - - - +
93D ILE* 4.1 17.5 - - + +
94D GLY* 3.8 26.8 - - - +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 5.1 2.9 - - + -
36C ILE* 4.4 13.2 - - + -
40C VAL* 4.9 1.8 - - + -
41C ALA* 3.8 31.6 - - + +
44C ILE* 3.9 39.0 - - + -
45C VAL* 4.2 6.5 - - + -
48C LEU* 4.7 1.1 - - + -
62C LEU* 5.0 3.4 - - + -
73C ALA 3.7 9.6 - - - +
74C GLY 3.1 7.4 + - - +
76C ALA* 1.3 73.8 - - - +
78C TYR* 1.3 67.5 + - - +
80C THR* 3.1 3.0 + - - -
81C ILE* 2.9 46.4 + - + +
103C LEU* 4.0 26.7 - - + -
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLY 2.8 18.9 + - - +
75C PHE* 3.8 15.0 - + + +
77C ILE* 1.3 76.0 - - - +
79C ASP* 1.3 80.5 + - - +
81C ILE* 3.2 7.5 + - - +
82C GLN* 3.0 44.7 + - + +
102C PHE* 3.5 18.8 - + + -
103C LEU* 3.8 11.6 - - + +
106C ALA* 3.4 33.7 - - + -
153C ILE* 3.3 32.0 - - + +
156C GLU* 5.3 1.9 + - - -
157C ARG* 3.3 20.6 + - - -
117D ASN* 3.7 13.7 - - - -
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE 2.8 21.1 + - - +
76C ALA* 4.3 2.2 - - - +
78C TYR* 1.3 84.5 - - - +
80C THR* 1.3 56.4 + - - +
82C GLN* 3.3 5.7 + - - +
83C HIS* 2.9 30.0 + - - +
93D ILE* 6.3 0.2 - - - -
94D GLY 5.8 0.7 + - - -
115D LEU* 3.4 28.9 - - + +
116D PRO* 3.8 12.8 - - + +
117D ASN* 2.6 57.8 + - - +
118D ALA 3.4 4.0 + - - -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 3.5 32.0 - - + +
48C LEU* 3.8 28.9 - - + -
49C LEU* 4.4 9.0 - - + -
76C ALA 2.8 21.4 + - - -
77C ILE 3.1 4.7 + - - -
79C ASP* 1.3 74.5 - - - +
81C ILE* 1.3 66.7 + - - +
83C HIS* 3.1 14.1 + - + +
84C ILE* 3.1 25.2 + - + +
93D ILE* 4.5 4.5 - - - +
115D LEU* 4.3 9.6 - - - +
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Residues in contact with ILE 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.8 16.6 - - + -
62C LEU* 4.1 21.8 - - + -
77C ILE* 2.9 35.3 + - + +
78C TYR* 3.5 10.3 - - - +
80C THR* 1.3 77.7 - - - +
82C GLN* 1.3 68.9 + - - +
83C HIS 3.2 0.2 + - - -
84C ILE* 3.5 21.4 + - - +
86C PRO 4.8 1.4 - - - +
88C VAL* 3.8 32.7 - - + +
90C THR* 5.2 2.2 - - + -
103C LEU* 4.8 9.9 - - + +
106C ALA* 3.9 26.9 - - + +
107C GLY* 5.1 0.9 - - - -
108C ALA 5.6 1.1 - - - +
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Residues in contact with GLN 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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78C TYR* 3.0 55.9 + - + +
79C ASP* 3.8 7.0 - - - +
80C THR 3.3 0.2 - - - -
81C ILE* 1.3 83.1 + - - +
83C HIS* 1.3 61.2 + - - +
84C ILE 3.5 4.7 + - - +
106C ALA* 3.1 25.2 + - - +
107C GLY 6.0 0.4 - - - -
108C ALA* 6.3 0.6 - - - +
157C ARG* 3.6 21.7 + - - +
116D PRO* 6.5 0.2 - - + -
192D PRO* 3.8 31.5 - - + +
193D GLU 4.3 4.9 + - - -
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Residues in contact with HIS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 5.3 7.4 - - + +
52C GLN* 5.8 3.6 - - - -
79C ASP 2.9 17.9 + - - +
80C THR* 3.1 9.5 + - - +
82C GLN* 1.3 80.2 - - - +
84C ILE* 1.3 69.8 + - - +
63D TYR* 5.6 4.9 - - - -
115D LEU* 4.4 11.5 - - + +
116D PRO* 6.3 1.1 - - + -
190D MET* 3.4 48.8 - - + +
191D VAL 4.5 12.1 - - - -
192D PRO* 4.6 3.8 - - + -
193D GLU* 3.9 34.7 + - + +
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Residues in contact with ILE 84 (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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48C LEU* 4.1 21.1 - - + +
49C LEU* 4.2 19.3 - - + -
52C GLN* 3.4 29.8 - - + +
60C ILE* 3.8 30.1 - - + -
80C THR* 3.1 21.5 + - + +
81C ILE* 3.5 13.8 - - - +
82C GLN 4.0 4.2 - - - +
83C HIS* 1.3 85.9 - - - +
85C LYS* 1.3 65.7 + - - +
86C PRO* 3.8 14.0 - - + +
88C VAL* 3.9 14.8 - - + -
193D GLU* 5.6 3.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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