Contacts of the helix formed by residues 84 - 102 (chain C) in PDB entry 3MGV
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 ALA 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C GLY 3.8 2.0 + - - -
83C LEU* 1.3 74.8 - - - +
85C VAL* 1.3 67.0 + - - +
86C LYS 4.3 2.5 - - - +
87C THR* 2.9 16.2 + - - +
88C ILE* 3.0 12.5 + - - +
129C GLU* 3.4 19.1 - - + +
13L T 2.9 45.2 + - - +
14L A 4.9 4.9 - - - +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 4.1 16.4 - - + +
84C ALA* 1.3 70.1 - - - +
86C LYS* 1.3 58.6 + - - +
88C ILE* 3.0 13.7 + - - +
89C GLN* 2.9 45.8 + - + +
117C MET* 5.0 4.7 - - + +
120C ILE* 4.6 3.8 - - + +
121C ARG* 3.8 38.1 - - + +
124C ASN* 3.8 28.7 - - + +
125C VAL* 5.4 0.2 - - + -
129C GLU* 2.8 23.1 + - - +
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 5.9 2.2 + - - +
84C ALA* 3.2 1.0 - - + +
85C VAL* 1.3 80.6 - - - +
87C THR* 1.3 59.7 + - - +
89C GLN* 3.5 25.4 + - - +
90C GLN* 3.1 21.1 + - - +
129C GLU* 4.8 0.4 + - - -
6K G 3.4 16.0 + - - -
7K C 4.2 4.2 - - - +
13L T 4.2 5.4 - - + +
14L A 3.3 58.6 + - + +
15L G 2.6 39.3 + - - -
1M C 4.5 3.0 - - - +
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.9 23.8 - - + -
84C ALA* 2.9 10.6 + - - +
86C LYS* 1.3 74.8 - - - +
88C ILE* 1.3 66.9 + - - +
90C GLN* 3.1 11.3 + - - +
91C HIS* 3.1 30.0 + - + +
12L A 3.4 14.5 - - + +
13L T 2.6 67.0 + - + +
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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
----------------------------------------------------------
75C LEU* 3.9 29.5 - - + +
78C LEU* 4.0 21.3 - - + -
79C GLN* 3.7 28.7 - - + +
83C LEU* 3.7 22.7 - - + +
84C ALA 3.0 11.1 + - - +
85C VAL* 3.4 8.1 - - - +
87C THR* 1.3 76.0 - - - +
89C GLN* 1.3 62.5 + - - +
91C HIS* 3.2 4.7 + - - +
92C LEU* 3.0 21.1 + - - +
117C MET* 3.9 20.9 - - + -
120C ILE* 3.9 22.0 - - + -
124C ASN* 4.6 2.9 - - - +
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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
----------------------------------------------------------
85C VAL* 2.9 27.4 + - - +
86C LYS* 3.7 41.5 - - + +
88C ILE* 1.3 73.0 - - - +
90C GLN* 1.3 54.3 + - - +
92C LEU* 3.4 5.7 + - + +
93C GLY* 2.7 33.8 + - - -
117C MET* 3.8 20.8 - - + +
121C ARG* 4.2 15.6 + - - -
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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
----------------------------------------------------------
44C MET* 4.1 15.9 - - + -
48C VAL* 4.4 3.6 - - + -
86C LYS 3.1 13.0 + - - +
87C THR 3.1 10.9 + - - +
89C GLN* 1.3 77.2 - - - +
91C HIS* 1.3 57.1 + - + +
93C GLY* 3.3 2.4 + - - +
94C GLN* 2.9 75.2 + - + +
7K C 5.0 7.8 - - - +
8K T 2.8 30.2 + - - +
9K A 4.4 0.9 + - - -
13L T 3.0 36.7 - - + +
14L A 3.5 6.4 + - - +
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Residues in contact with HIS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C MET* 5.9 1.2 - - - +
47C SER 5.3 0.7 - - - -
48C VAL* 3.7 32.9 - - + +
51C SER* 3.8 17.3 - - - -
74C TYR* 2.6 35.4 + - + -
75C LEU* 4.9 1.1 - - + -
78C LEU* 3.5 26.8 - - + +
83C LEU* 4.6 0.8 - - - +
87C THR* 3.1 41.1 + - + +
88C ILE 3.2 7.4 + - - +
90C GLN* 1.3 77.5 - - + +
92C LEU* 1.3 63.1 + - - +
94C GLN 3.4 0.7 + - - -
95C LEU* 3.1 29.6 + - - +
11L T 6.2 0.2 - - - +
12L A 4.4 13.4 + - - -
13L T 5.3 2.1 - - + +
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Residues in contact with LEU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 4.5 5.8 - - + -
75C LEU* 4.1 15.7 - - + +
88C ILE 3.0 12.9 + - - +
89C GLN* 3.7 9.0 - - + +
91C HIS* 1.3 75.7 - - - +
93C GLY* 1.3 53.7 + - - +
95C LEU* 3.2 5.9 + - + -
96C ASN* 2.7 49.2 + - - +
107C PRO* 3.9 10.1 - - + -
108C SER* 3.2 32.3 - - - +
113C VAL* 3.8 22.0 - - + -
117C MET* 3.7 33.4 - - + -
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Residues in contact with GLY 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLN 2.7 21.6 + - - -
90C GLN* 3.7 3.4 - - - -
92C LEU* 1.3 73.1 - - - +
94C GLN* 1.3 59.2 + - - +
96C ASN* 3.4 12.2 + - - +
97C MET* 3.0 27.4 + - - +
6K G 5.6 7.3 - - - +
7K C 4.3 7.5 + - - -
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR 4.0 4.6 + - - -
44C MET* 3.9 13.0 - - - +
45C LEU* 3.4 36.5 - - + +
48C VAL* 3.8 30.7 - - + -
49C CYS* 6.3 0.2 - - - -
90C GLN* 2.9 44.2 + - - +
91C HIS 3.9 0.7 - - - +
93C GLY* 1.3 75.2 - - - +
95C LEU* 1.3 65.2 + - - +
97C MET* 3.1 34.1 + - - +
98C LEU 3.1 19.1 + - - -
7K C 5.9 0.8 - - - -
8K T 3.7 18.2 - - - +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 4.4 7.9 - - + -
49C CYS* 5.0 5.8 - - - -
52C TRP* 3.7 51.8 - - + +
66C ALA* 5.3 0.7 - - + -
71C VAL* 4.5 21.3 - - + -
74C TYR* 4.4 15.3 - - + -
75C LEU* 6.0 0.2 - - + -
91C HIS 3.1 18.3 + - - +
92C LEU* 3.7 7.6 - - - +
94C GLN* 1.3 73.5 - - - +
96C ASN* 1.3 64.8 + - - +
98C LEU* 3.4 12.8 + - + +
99C HIS* 2.8 42.3 + - + +
107C PRO* 4.2 13.5 - - + -
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Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 2.7 30.6 + - - +
93C GLY* 3.5 10.5 - - - +
95C LEU* 1.3 72.5 - - - +
97C MET* 1.3 57.4 + - - +
99C HIS* 3.3 2.4 + - - +
100C ARG* 2.8 30.6 + - - +
106C ARG* 3.5 31.4 - - - +
107C PRO* 3.3 15.1 - - - +
108C SER* 2.8 51.3 + - - -
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Residues in contact with MET 97 (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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30C MET* 4.8 8.1 - - + -
37C PHE* 4.0 36.1 - - - -
41C THR* 3.6 25.6 - - + -
45C LEU* 5.1 8.3 - - + -
93C GLY 3.0 16.5 + - - +
94C GLN* 3.1 33.6 + - - +
96C ASN* 1.3 71.8 - - - +
98C LEU* 1.3 68.8 + - - +
100C ARG* 4.5 4.9 - - - +
101C ARG* 3.0 34.3 + - + +
7K C 3.7 31.2 - - + +
8K T 5.8 0.4 - - + -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 4.0 18.1 - - + +
30C MET* 5.2 7.0 - - + -
45C LEU* 4.4 14.8 - - + +
49C CYS* 3.8 25.1 - - - -
63C TRP* 4.2 18.8 - - + -
64C PHE* 3.9 20.2 - - + -
94C GLN 3.1 12.4 + - - +
95C LEU* 3.7 14.6 - - + +
97C MET* 1.3 79.2 - - - +
99C HIS* 1.3 63.7 + - + +
101C ARG* 3.8 3.1 - - - +
102C SER* 2.8 43.3 + - - +
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C TRP 4.9 1.8 - - - -
64C PHE* 4.0 16.7 - + - -
65C PRO* 3.7 9.7 - - + +
66C ALA* 2.9 47.8 + - + +
95C LEU* 2.8 38.2 + - + +
96C ASN 3.8 3.1 - - - +
98C LEU* 1.3 81.1 - - + +
100C ARG* 1.3 66.6 + - - +
102C SER* 3.0 11.4 + - - -
104C LEU* 2.9 42.7 + - + +
105C PRO* 3.5 29.2 - - + +
106C ARG* 4.2 0.7 - - - -
107C PRO* 4.0 11.6 - - + +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN 2.8 22.0 + - - +
97C MET* 4.0 5.4 - - - +
99C HIS* 1.3 70.5 - - - +
101C ARG* 1.3 105.2 + - + +
103C GLY* 3.0 20.1 + - - -
104C LEU 4.1 6.3 + - - +
106C ARG* 4.2 23.6 - - + +
111D ASN* 5.4 0.7 + - - -
114D SER* 5.9 0.2 - - - -
6K G 4.0 24.1 + - - -
7K C 4.6 12.6 + - - -
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ASN* 3.3 13.2 - - - +
30C MET* 3.6 34.3 - - + +
37C PHE* 4.1 9.3 - - + -
97C MET* 3.0 28.0 + - + +
98C LEU 3.8 0.7 - - - +
100C ARG* 1.3 107.9 - - + +
102C SER* 1.3 56.1 + - - +
103C GLY 3.3 0.2 - - - -
111D ASN* 2.8 45.4 - - - +
114D SER* 2.7 31.1 + - - -
115D LEU* 3.6 27.4 - - - +
118D ARG* 4.1 19.6 - - - +
7K C 5.2 4.9 + - - -
4M A 6.0 2.8 - - - -
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 5.7 0.2 - - - +
23C VAL* 3.7 18.7 - - - +
26C ASN* 2.9 24.8 + - - -
27C LEU* 3.7 17.0 - - - +
64C PHE* 3.3 19.4 - - - -
98C LEU* 2.8 20.3 + - - +
99C HIS 3.0 7.9 + - - -
101C ARG* 1.3 76.0 - - - +
103C GLY* 1.3 59.2 + - - +
104C LEU* 3.8 22.2 - - - +
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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
------------------------------------------------------------
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