Contacts of the helix formed by residues 104 - 111 (chain B) in PDB entry 3F7G
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 PRO 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B GLU 4.5 3.1 - - - +
103B VAL* 1.3 88.2 - - + +
105B PRO* 1.3 71.1 - - + +
106B GLU* 3.1 21.1 + - + +
107B LEU* 3.1 34.8 + - + +
108B LEU* 3.3 10.4 + - - +
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Residues in contact with PRO 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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91B LEU* 4.1 12.1 - - + -
94B PHE* 3.4 37.7 - - + +
97B TRP* 3.7 25.4 - - + -
103B VAL 3.5 4.7 - - - +
104B PRO* 1.3 82.4 - - + +
106B GLU* 1.3 65.5 + - - +
108B LEU* 3.1 10.3 + - + +
109B ALA* 2.7 38.2 + - - +
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Residues in contact with GLU 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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87B GLU* 4.4 3.9 - - - +
91B LEU* 4.6 20.9 - - + +
104B PRO* 3.2 22.9 - - + +
105B PRO* 1.3 89.3 - - - +
107B LEU* 1.3 59.4 + - + +
109B ALA* 4.0 4.1 - - - +
110B ALA* 3.0 30.0 + - - +
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Residues in contact with LEU 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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103B VAL* 5.3 0.7 - - + -
104B PRO* 3.1 33.2 + - + +
106B GLU* 1.3 78.0 - - + +
108B LEU* 1.3 67.6 + - - +
110B ALA* 3.4 7.9 + - + +
111B ALA* 3.1 24.1 + - - +
138B ASP 5.6 1.6 - - - +
139B ASP* 5.1 8.5 - - - +
140B PRO* 3.8 24.8 - - + +
141B TRP* 5.6 3.2 + - + -
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Residues in contact with LEU 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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94B PHE* 3.8 20.0 - - + -
97B TRP* 3.5 36.1 - - + -
103B VAL* 3.7 27.8 - - + +
104B PRO 3.3 4.0 + - - +
105B PRO* 3.1 7.3 + - + +
107B LEU* 1.3 78.6 - - - +
109B ALA* 1.3 59.5 + - - +
111B ALA 3.2 8.3 + - - -
112B GLY 3.4 0.5 + - - -
113B PHE* 3.0 37.6 + - + +
122B VAL* 4.6 1.8 - - + -
134B TRP* 3.6 42.6 - - + +
140B PRO* 3.8 13.0 - - + -
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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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87B GLU* 4.0 13.7 - - + +
90B ARG* 2.8 35.8 + - + +
91B LEU* 3.9 37.0 - - + +
94B PHE* 4.3 2.0 - - + -
105B PRO 2.7 20.0 + - - +
106B GLU 4.0 2.9 - - - +
108B LEU* 1.3 71.2 - - - +
110B ALA* 1.3 62.4 + - - +
112B GLY 3.0 2.3 + - - -
113B PHE 3.4 10.8 - - - +
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Residues in contact with ALA 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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87B GLU* 3.7 26.3 + - - +
90B ARG* 4.1 0.7 + - - -
106B GLU 3.0 18.3 + - - +
107B LEU* 3.8 9.2 - - + +
109B ALA* 1.3 76.7 - - - +
111B ALA* 1.3 57.6 + - - +
112B GLY 3.3 3.3 + - - -
141B TRP* 3.2 24.2 - - - +
153B PHE* 3.9 9.7 - - - -
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Residues in contact with ALA 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 LEU 3.1 17.4 + - - +
108B LEU 3.6 3.4 - - - +
109B ALA 3.1 0.6 - - - -
110B ALA* 1.3 74.4 - - - +
112B GLY* 1.3 57.0 + - - +
113B PHE* 3.4 9.4 + - + -
140B PRO* 3.5 23.3 - - + -
141B TRP* 3.6 32.1 - - + +
144B HIS* 2.7 32.6 + - - -
153B PHE* 3.8 4.9 - - - -
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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