Contacts of the helix formed by residues 102 - 114 (chain B) in PDB entry 3VF0
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 ASN 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ASN* 4.3 1.1 - - - +
59B ARG* 3.4 20.1 - - - +
100B LEU* 3.4 1.3 - - - +
101B LEU* 1.3 97.2 - - - +
103B GLY* 1.3 62.5 + - - +
104B GLU* 3.2 11.1 + - - +
105B GLN* 3.0 40.0 + - - +
106B ALA 3.3 14.4 + - - -
3004B GOL 3.2 29.7 + - - +
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG 3.7 15.9 - - - -
58B ARG 3.5 20.1 - - - +
59B ARG* 4.0 1.8 - - - +
102B ASN* 1.3 68.8 - - - +
104B GLU* 1.4 58.0 + - - +
106B ALA* 3.4 3.0 + - - +
107B GLU* 3.0 34.2 + - - +
3004B GOL 2.7 20.6 + - - -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASN* 3.2 12.5 + - - +
103B GLY* 1.4 74.7 - - - +
105B GLN* 1.3 59.6 + - + +
107B GLU* 3.7 4.9 + - - +
108B ALA* 3.1 27.0 + - - +
3004B GOL 3.2 27.9 + - - +
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASP 4.5 3.0 + - - -
82B TYR* 3.8 22.1 - - + +
83B GLU* 3.3 32.3 + - - +
100B LEU* 3.7 13.3 - - + +
101B LEU* 3.2 36.5 + - + +
102B ASN* 3.0 28.0 + - - +
103B GLY 3.3 0.2 - - - -
104B GLU* 1.3 74.6 - - + +
106B ALA* 1.4 54.2 + - - +
108B ALA* 3.2 8.0 + - - +
109B ALA* 2.8 35.2 + - - +
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG 3.3 26.2 - - - +
59B ARG* 3.8 16.4 - - - +
61B ILE* 3.9 16.2 - - + +
100B LEU* 3.7 12.0 - - - +
102B ASN 3.3 3.4 + - - +
103B GLY 3.5 3.8 - - - +
105B GLN* 1.4 77.4 - - - +
107B GLU* 1.4 56.5 + - + +
109B ALA* 3.3 4.0 + - - +
110B ILE* 3.0 35.0 + - - +
127B LEU* 4.1 7.0 - - + -
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ARG 5.9 0.2 - - - +
103B GLY 3.0 20.5 + - - +
104B GLU* 4.1 5.8 - - - +
105B GLN 3.4 0.2 - - - -
106B ALA* 1.4 72.2 - - - +
108B ALA* 1.3 59.8 + - - +
110B ILE* 3.4 18.6 + - - +
111B ASN* 2.9 30.7 + - - +
127B LEU* 3.8 25.1 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 3.3 18.8 + - + +
104B GLU 3.1 20.1 + - - +
105B GLN* 3.2 6.7 + - - +
107B GLU* 1.3 77.0 - - - +
109B ALA* 1.3 56.3 + - - +
111B ASN* 4.0 5.5 + - - +
112B ALA* 3.0 30.7 + - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.3 15.0 - - + -
79B LEU* 4.3 7.9 - - + -
82B TYR* 3.7 22.4 + - + -
100B LEU* 3.9 17.7 - - + -
105B GLN 2.8 19.5 + - - +
106B ALA 3.6 5.2 - - - +
108B ALA* 1.3 69.9 - - - +
110B ILE* 1.4 55.8 + - - +
113B PHE* 2.8 41.7 + - - +
125B VAL* 4.2 3.5 - - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 4.1 10.1 - - + -
106B ALA 3.0 20.9 + - - +
107B GLU* 3.7 20.9 - - - +
108B ALA 3.3 0.2 - - - -
109B ALA* 1.4 71.3 - - - +
111B ASN* 1.3 62.1 + - - +
114B HIS* 2.8 38.8 + - + +
125B VAL* 3.5 34.5 - - + +
126B GLN* 4.1 10.5 - - - +
127B LEU* 3.8 43.5 - - + +
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU 2.9 17.1 + - - +
108B ALA* 4.0 6.3 + - - +
110B ILE* 1.3 78.6 - - - +
112B ALA* 1.3 66.2 + - - +
114B HIS 4.4 6.2 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 3.8 13.7 - - - +
108B ALA 3.0 20.4 + - - +
111B ASN* 1.3 83.6 - - - +
113B PHE* 1.3 82.7 + - + +
114B HIS 5.1 0.9 - - - +
116B SER* 4.2 7.3 - - - -
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU* 3.3 52.5 - - + -
79B LEU* 4.1 16.6 - - + -
81B ASP* 6.1 1.3 - - - -
82B TYR* 3.8 24.2 - + - -
109B ALA* 2.8 30.3 + - + +
112B ALA* 1.3 90.1 - - + +
114B HIS* 1.3 65.3 + - - +
115B GLN 3.2 0.9 + - - -
116B SER* 2.7 32.9 + - - +
123B LEU* 4.0 8.1 - - + +
125B VAL* 3.6 20.7 - - + +
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ILE* 2.8 29.2 + - + +
111B ASN 4.4 5.4 + - - +
112B ALA 5.1 0.7 - - - +
113B PHE* 1.3 70.5 - - - +
115B GLN* 1.3 100.0 + - + +
116B SER* 3.3 1.6 + - - -
123B LEU 4.7 0.2 - - - -
124B SER* 3.5 25.1 - - - -
125B VAL* 2.9 41.0 + - - +
126B GLN* 3.4 23.2 + - + -
3008B GOL 5.1 2.0 - - - -
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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