Contacts of the helix formed by residues 100 - 114 (chain G) in PDB entry 3VON
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 GLN 100 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C GLN* 4.1 12.6 - - - +
44C ASP* 3.2 37.7 + - - +
7G ARG* 4.1 3.8 - - - +
11G GLU* 3.3 26.3 + - - +
14G ARG* 3.6 18.4 - - - +
62G TYR* 3.9 3.4 - - - -
95G TRP* 4.4 3.6 - - - -
98G ALA 5.5 1.0 - - - +
99G LEU* 1.3 79.4 - - - +
101G ILE* 1.3 58.1 + - - +
102G ARG* 3.6 28.0 - - + +
103G THR* 2.7 43.7 + - - +
104G VAL* 3.3 9.5 + - - +
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Residues in contact with ILE 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G GLU* 3.2 36.2 + - + +
15G LEU* 4.4 23.3 - - + -
35G PHE* 4.8 10.1 - - + -
56G LEU* 4.1 24.9 - - + -
58G LEU* 3.6 40.6 - - + -
62G TYR* 3.4 14.8 + - + +
67G PRO* 4.9 2.9 - - + -
95G TRP* 5.2 0.2 - - - -
100G GLN* 1.3 71.3 - - - +
102G ARG* 1.3 62.4 + - - +
104G VAL* 3.2 13.7 + - - +
105G LEU* 3.1 27.7 + - + +
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Residues in contact with ARG 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASP* 5.4 0.7 - - - -
11G GLU* 5.1 0.6 + - - -
14G ARG* 4.6 11.6 - - - +
15G LEU* 4.9 14.3 - - + +
18G GLU* 2.8 51.2 + - - +
19G PRO 4.2 1.6 + - - -
20G VAL* 3.5 28.5 - - + +
100G GLN* 3.6 28.6 - - + +
101G ILE* 1.3 75.9 - - - +
103G THR* 1.3 57.0 + - - +
105G LEU* 3.1 9.5 + - + +
106G LEU* 2.8 58.4 + - + +
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Residues in contact with THR 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLN* 3.7 12.6 + - - +
90G ILE* 4.5 8.1 - - + -
99G LEU* 4.0 28.1 - - + +
100G GLN* 2.7 36.3 + - - +
102G ARG* 1.3 74.0 - - - +
104G VAL* 1.3 52.5 + - - -
106G LEU* 3.6 7.2 - - + +
107G SER* 2.7 39.5 + - - +
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Residues in contact with VAL 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LEU* 4.4 9.2 - - + -
67G PRO* 4.0 22.4 - - + -
69G VAL* 4.0 21.8 - - + -
88G LEU* 5.3 0.2 - - + -
90G ILE* 4.0 19.9 - - + +
91G LEU* 4.0 14.1 - - + -
95G TRP* 4.3 13.0 - - + -
100G GLN 3.8 10.8 - - - +
101G ILE* 3.3 8.7 - - - +
102G ARG 3.2 0.4 - - - -
103G THR* 1.3 76.0 - - - +
105G LEU* 1.3 62.6 + - - +
107G SER* 3.1 2.8 + - - -
108G ILE* 2.9 42.8 + - + +
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.4 18.2 - - + -
20G VAL* 5.6 4.5 - - + -
23G ILE* 3.8 40.5 - - + +
25G ALA* 4.0 18.4 - - + -
37G VAL* 4.5 16.2 - - + -
39G ILE* 4.7 5.3 - - + +
54G LEU* 6.3 0.7 - - + -
56G LEU* 3.8 28.5 - - + -
69G VAL* 6.1 0.4 - - + -
101G ILE* 3.1 19.9 + - + +
102G ARG* 3.5 9.0 - - - +
104G VAL* 1.3 79.0 - - + +
106G LEU* 1.3 62.9 + - + +
108G ILE* 3.3 11.8 + - + +
109G GLN* 3.0 22.0 + - - +
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G VAL* 3.8 34.8 - - + -
102G ARG* 2.8 59.6 + - + +
103G THR* 3.6 7.6 - - + +
105G LEU* 1.3 75.2 - - + +
107G SER* 1.3 55.6 + - - +
109G GLN* 3.2 13.6 + - - +
110G ALA* 3.0 28.1 + - - +
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Residues in contact with SER 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G LEU* 4.2 14.8 - - - +
90G ILE* 3.5 28.3 - - - +
103G THR* 2.7 23.3 + - - +
104G VAL 3.3 5.6 - - - -
106G LEU* 1.3 71.5 - - - +
108G ILE* 1.3 63.8 + - - +
110G ALA* 3.4 7.4 + - - +
111G LEU* 3.1 25.8 + - - +
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Residues in contact with ILE 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G ILE* 3.6 23.8 - - + -
54G LEU* 4.0 6.3 - - + -
69G VAL* 3.9 29.2 - - + -
71G PHE* 4.0 24.5 - - + -
86G ILE* 3.9 17.5 - - + -
88G LEU* 4.1 16.4 - - + -
91G LEU* 5.0 0.7 - - + -
104G VAL* 2.9 32.2 + - + +
105G LEU* 3.8 9.0 - - + +
107G SER* 1.3 72.8 - - - +
109G GLN* 1.3 63.2 + - - +
111G LEU* 3.3 11.6 - - + +
112G LEU* 3.2 24.1 + - + +
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Residues in contact with GLN 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G VAL* 3.8 10.4 - - - +
21G PRO 3.2 23.2 + - - -
22G GLY* 4.1 10.5 - - - -
23G ILE* 3.2 24.6 - - + +
39G ILE* 4.3 18.6 - - + +
40G ALA 5.1 4.6 + - - +
42G PRO* 4.2 10.6 - - + +
105G LEU 3.0 11.5 + - - +
106G LEU* 3.3 17.0 - - - +
108G ILE* 1.3 77.2 - - - +
110G ALA* 1.3 65.3 + - - +
112G LEU* 3.1 7.9 + - - +
113G SER* 3.0 21.1 + - - -
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU 3.0 12.9 + - - +
107G SER* 3.6 10.8 - - - +
109G GLN* 1.3 75.3 - - - +
111G LEU* 1.3 57.9 + - + +
113G SER* 3.0 9.6 + - - -
114G ALA* 2.9 31.6 + - - +
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Residues in contact with LEU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PHE* 6.4 0.7 - - + -
77G HIS* 3.0 21.9 + - + -
79G ASN* 3.3 43.5 - - + +
80G VAL* 6.0 1.3 - - + -
86G ILE* 4.3 16.8 - - + -
87G CYS 4.7 0.9 - - - +
88G LEU* 4.1 30.7 - - + -
107G SER 3.1 10.0 + - - +
108G ILE* 3.3 16.2 - - + +
110G ALA* 1.3 79.8 - - + +
112G LEU* 1.3 61.9 + - + +
114G ALA 3.1 24.0 - - - +
115G PRO* 3.4 0.5 - - - +
116G ASN* 5.6 3.1 - - + +
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Residues in contact with LEU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ILE* 4.1 27.1 - - + -
40G ALA 4.7 0.4 - - - +
42G PRO* 3.9 22.2 - - + -
45G SER* 3.7 5.7 - - - -
47G PHE* 3.5 28.0 - - + -
52G PHE* 4.2 22.4 - - + -
71G PHE* 4.5 17.0 - - + -
75G ILE* 3.5 30.1 - - + -
77G HIS* 4.1 16.6 - - + -
80G VAL* 5.9 0.4 - - + -
108G ILE* 3.2 12.8 + - + +
109G GLN 3.1 7.9 + - - +
111G LEU* 1.3 77.5 - - + +
113G SER* 1.3 64.4 + - - +
114G ALA 3.4 0.3 + - - -
115G PRO* 3.8 3.5 - - - +
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Residues in contact with SER 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G PRO* 3.8 24.1 - - - +
43G GLN 5.0 3.3 + - - -
44G ASP 6.0 0.2 - - - -
45G SER* 4.4 10.3 - - - -
109G GLN* 3.0 11.9 + - - -
110G ALA* 3.0 13.5 + - - -
112G LEU* 1.3 78.8 - - - +
114G ALA* 1.3 60.0 + - - +
115G PRO* 4.0 2.4 - - - +
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Residues in contact with ALA 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ALA 2.9 11.6 + - - +
111G LEU* 3.1 11.8 - - - +
113G SER* 1.3 80.4 - - - +
115G PRO* 1.3 68.1 - - - +
116G ASN* 3.5 9.9 + - + +
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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