Contacts of the helix formed by residues 77 - 93 (chain C) in PDB entry 3M0V
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 GLY 77 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PRO 3.6 0.2 - - - -
76C ARG* 1.3 79.9 - - - +
78C ILE* 1.3 67.1 + - - -
79C PHE* 3.1 4.3 - - - -
80C ASP* 3.0 6.4 + - - +
81C LYS* 3.0 31.6 + - - +
104C TRP 5.7 2.7 - - - -
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER* 4.0 11.9 - - - -
77C GLY* 1.3 71.6 - - - -
79C PHE* 1.3 72.3 + - + +
81C LYS* 3.3 8.2 + - + +
82C LEU* 2.8 41.0 + - + +
100C LEU* 3.4 28.9 - - + -
104C TRP 5.1 3.8 + - - -
105C ASP* 3.5 43.8 + - + +
106C LYS 5.1 0.4 - - - +
107C ALA* 4.2 7.9 - - + -
112C LEU* 3.7 32.1 - - + -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLY* 3.1 1.7 + - - -
78C ILE* 1.3 82.2 - - + +
80C ASP* 1.3 68.1 + - - +
82C LEU* 3.3 8.4 + - + +
83C ASP* 3.1 28.0 + - - +
107C ALA* 4.1 25.1 - - + -
111C GLU* 3.8 52.0 - - + -
112C LEU* 4.0 13.9 - - + -
115C ARG* 4.3 20.7 - - + +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PRO* 3.5 22.3 - - + +
76C ARG* 2.6 65.7 + - - +
77C GLY 3.0 5.0 + - - +
79C PHE* 1.3 78.7 - - - +
81C LYS* 1.3 63.8 + - - +
83C ASP* 3.0 15.0 + - - +
84C ASP* 3.0 18.4 + - - -
419C ARG* 3.6 25.0 + - - +
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Residues in contact with LYS 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C SER* 3.2 32.5 + - - +
57C TRP* 4.1 12.5 - - - +
59C VAL* 3.8 18.7 - - + +
60C GLY* 4.8 6.7 - - - +
75C PRO* 3.7 29.2 - - + -
76C ARG 5.8 0.4 - - - -
77C GLY* 3.0 24.7 + - - +
78C ILE* 3.6 16.8 - - + +
80C ASP* 1.3 76.5 - - - +
82C LEU* 1.3 56.6 + - - +
84C ASP* 3.2 2.6 + - - +
85C CYS* 2.9 35.1 + - - -
104C TRP* 5.3 4.9 + - - +
105C ASP* 4.2 12.5 + - - +
430D ILE* 5.2 14.6 - - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ILE* 2.8 48.1 + - + +
79C PHE* 3.6 7.6 - - + +
80C ASP 3.2 0.2 - - - -
81C LYS* 1.3 76.5 - - - +
83C ASP* 1.3 63.8 + - - +
85C CYS* 3.2 3.2 + - - -
86C ALA 3.0 18.0 + - - -
98C VAL* 4.2 24.0 - - + -
112C LEU* 4.4 20.2 - - + +
115C ARG* 4.1 25.8 - - + -
116C GLY* 4.7 2.9 - - - +
119C LEU* 3.4 19.8 - - + +
121C LEU* 3.5 9.7 - - + +
123C PHE* 4.0 24.5 - - + -
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Residues in contact with ASP 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 2.9 52.3 + - - +
79C PHE* 3.1 14.4 + - - +
80C ASP* 3.0 18.1 + - - +
82C LEU* 1.3 77.0 - - - +
84C ASP* 1.3 62.3 + - - +
86C ALA* 3.1 10.2 - - - +
87C VAL* 3.6 1.0 + - - +
115C ARG* 2.7 43.4 + - - -
119C LEU* 3.6 6.5 - - - +
411C TYR* 3.8 0.9 - - - +
419C ARG* 4.4 3.0 + - - +
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 3.4 30.7 - - + +
75C PRO* 4.0 8.3 - - - +
80C ASP 3.0 9.4 + - - +
81C LYS 3.2 1.1 + - - +
83C ASP* 1.3 74.9 - - - +
85C CYS* 1.3 63.7 + - - +
87C VAL* 3.1 19.4 + - - +
88C ILE* 3.5 11.0 + - - +
336C ILE* 3.8 23.9 - - + +
411C TYR* 2.6 32.5 + - - -
412C ARG* 4.7 3.2 + - - -
419C ARG* 2.9 37.8 + - - -
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Residues in contact with CYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.8 24.0 - - + -
55C PRO 5.0 0.2 - - - -
56C SER* 5.0 0.7 - - - -
59C VAL* 3.4 25.1 - - - -
81C LYS 2.9 25.5 + - - +
82C LEU* 3.2 5.8 + - - +
84C ASP* 1.3 74.1 - - - +
86C ALA* 1.3 65.9 + - - +
88C ILE* 3.1 13.8 + - - +
89C GLN* 3.0 23.4 + - - +
95C THR* 4.6 1.4 + - - +
98C VAL* 3.9 32.5 - - + -
121C LEU* 4.0 4.8 - - + +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.6 15.9 - - + -
82C LEU 3.0 12.3 + - - +
83C ASP 3.1 15.0 - - - +
84C ASP 3.1 0.4 - - - -
85C CYS* 1.3 78.2 - - - +
87C VAL* 1.3 54.1 + - - +
89C GLN* 3.5 2.6 + - - +
90C GLN* 2.9 29.7 + - - +
119C LEU* 3.9 31.8 - - + +
121C LEU* 3.8 11.6 - - - +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ARG* 3.3 28.7 - - + -
6C ILE* 3.8 23.6 - - + -
83C ASP 3.9 0.7 - - - +
84C ASP 3.3 11.0 - - - +
85C CYS 3.1 0.4 - - - -
86C ALA* 1.3 75.1 - - - +
88C ILE* 1.3 66.5 + - - +
90C GLN* 3.2 5.5 + - - +
91C LEU* 2.9 37.6 + - + +
336C ILE* 4.2 7.9 - - + -
340C ILE* 5.2 0.2 - - + -
406C TYR* 3.9 16.8 - - + -
411C TYR* 3.6 29.8 - - + -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 4.4 8.5 - - + -
59C VAL* 5.4 1.8 - - + -
84C ASP 3.7 9.2 - - - +
85C CYS* 3.1 22.6 + - - +
87C VAL* 1.3 75.3 - - - +
89C GLN* 1.3 54.3 + - - +
92C THR* 2.7 43.4 + - + +
95C THR* 3.4 25.6 - - + +
336C ILE* 3.9 26.7 - - + +
339C LEU* 3.5 39.0 - - + +
340C ILE* 4.1 27.8 - - + +
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Residues in contact with GLN 89 (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 PHE* 5.6 1.8 - - - -
85C CYS 3.0 13.9 + - - +
86C ALA* 3.8 3.6 - - - +
88C ILE* 1.3 75.5 - - - +
90C GLN* 1.3 61.7 + - - +
92C THR* 4.1 0.4 - - - -
93C ARG* 2.7 54.8 + - - +
94C ALA 3.3 4.9 + - - -
95C THR* 2.9 46.7 + - - +
96C PRO* 3.1 27.1 - - + +
119C LEU 5.6 2.2 - - - +
120C GLY 4.5 8.4 + - - +
121C LEU* 3.9 12.8 - - + -
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Residues in contact with GLN 90 (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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4C PHE* 3.7 21.7 - - + -
5C ARG* 3.3 12.8 + - - +
6C ILE* 3.0 57.7 + - - +
8C GLN* 5.2 0.8 - - - +
11C VAL* 3.7 16.2 - - - +
86C ALA 2.9 18.7 + - - +
87C VAL* 3.2 4.5 + - - +
89C GLN* 1.3 78.4 - - - +
91C LEU* 1.3 62.9 - - + +
93C ARG* 3.0 40.1 + - - +
397C GLY 3.5 3.7 + - - +
398C GLY* 3.4 8.8 - - - -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.2 16.8 - - + -
11C VAL* 4.2 12.8 - - + -
87C VAL* 2.9 32.5 + - + +
88C ILE 4.2 1.1 - - - +
90C GLN* 1.3 81.8 - - - +
92C THR* 1.3 60.7 + - + +
340C ILE* 4.1 7.4 - - + -
393C ARG* 3.5 8.8 - - - -
398C GLY* 3.5 2.6 - - - -
399C ALA* 3.0 32.2 + - + +
402C PRO* 3.6 34.1 - - + +
405C THR* 3.9 22.9 - - + -
406C TYR* 3.8 24.5 - - + -
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Residues in contact with THR 92 (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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88C ILE* 2.7 31.8 + - + +
91C LEU* 1.3 75.3 - - - +
93C ARG* 1.3 73.3 + - - +
94C ALA* 3.0 18.2 + - - +
95C THR* 3.8 8.1 + - - +
340C ILE* 3.5 45.1 - - + +
343C ALA* 5.0 2.7 - - + -
344C ASN* 3.9 18.3 + - - +
347C ARG* 3.8 8.0 + - - -
393C ARG* 3.5 21.6 - - - +
402C PRO* 4.3 1.3 - - + -
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Residues in contact with ARG 93 (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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4C PHE* 4.7 13.7 - - - -
48C GLU 4.5 0.7 - - - +
51C PHE* 3.5 12.5 - - - -
89C GLN* 2.7 48.8 + - - +
90C GLN* 3.0 34.8 + - - +
92C THR* 1.3 74.6 + - - +
94C ALA* 1.3 55.8 + - - +
347C ARG* 2.9 17.0 + - - +
393C ARG* 4.5 0.7 - - - +
396C THR* 3.3 48.0 + - - +
397C GLY* 3.3 20.2 + - - -
398C GLY* 3.7 16.6 - - - +
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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
------------------------------------------------------------
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