Contacts of the helix formed by residues 102 - 112 (chain W) in PDB entry 6FF7
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 GLU 102 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100W LEU* 4.0 1.1 - - - +
101W VAL* 1.3 79.2 - - + +
103W LEU* 1.3 55.1 + - - +
104W GLY* 4.2 5.6 - - - +
105W ASP* 2.6 41.1 + - + +
106W LEU* 3.8 2.3 + - - +
125W VAL* 4.7 4.8 - - - +
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Residues in contact with LEU 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101W VAL 4.1 1.0 + - - -
102W GLU* 1.3 70.4 - - - +
104W GLY* 1.3 59.9 + - - +
106W LEU* 3.1 24.0 + - - +
107W ASP* 3.9 2.3 + - - -
125W VAL* 4.9 7.3 - - - +
128W LYS* 5.6 11.4 - - + +
131W TYR* 6.0 4.5 - - + -
134W TYR* 4.9 16.8 - - + -
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Residues in contact with GLY 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102W GLU* 2.9 5.3 + - - +
103W LEU* 1.3 76.3 - - - +
105W ASP* 1.3 59.6 + - - +
106W LEU 3.2 1.1 - - - -
107W ASP* 3.2 24.5 - - - +
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Residues in contact with ASP 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77W CYS 4.4 16.8 - - - +
78W ARG* 5.2 4.0 - - + -
79W ILE* 4.0 24.3 + - - +
100W LEU* 5.3 9.0 - - + -
101W VAL 5.3 0.7 - - - +
102W GLU* 2.6 33.3 + - + +
104W GLY* 1.3 71.7 - - - -
106W LEU* 1.3 55.2 - - - -
107W ASP 3.3 0.6 + - - -
108W PRO* 4.6 3.2 - - - +
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Residues in contact with LEU 106 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W ILE* 5.7 2.0 - - - -
102W GLU 3.8 1.7 + - - +
103W LEU* 3.1 14.7 + - - +
105W ASP* 1.3 76.1 - - - +
107W ASP* 1.3 65.1 + - - +
108W PRO 3.4 1.3 - - - -
109W LEU* 3.2 23.8 + - + +
110W ALA 4.5 0.3 + - - -
135W VAL* 6.3 4.0 - - + -
138W LYS* 6.1 1.0 - - - +
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Residues in contact with ASP 107 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103W LEU 3.9 1.6 + - - +
104W GLY* 3.2 22.4 + - - +
105W ASP 3.3 1.2 - - - -
106W LEU* 1.3 77.4 - - - +
108W PRO* 1.3 57.0 - - - +
109W LEU 2.8 6.9 + - - -
110W ALA* 3.0 22.6 + - - +
138W LYS* 5.6 9.6 - - + -
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Residues in contact with PRO 108 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W ILE* 3.7 24.7 - - + +
80W GLY 3.4 27.2 - - - +
81W GLU* 4.5 9.7 - - + +
83W LEU* 5.3 7.5 - - + +
105W ASP 4.6 2.5 - - - +
106W LEU 3.3 1.2 - - - -
107W ASP* 1.3 74.3 - - - +
109W LEU* 1.3 57.2 + - - +
110W ALA 3.2 1.4 + - - -
111W SER* 3.6 17.7 + - - -
112W LEU* 4.6 1.7 + - - +
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Residues in contact with LEU 109 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W ILE* 5.6 1.0 - - - +
106W LEU* 3.2 16.0 + - + +
107W ASP 2.8 1.6 + - - -
108W PRO* 1.3 72.8 - - - +
110W ALA* 1.3 64.1 + - - +
111W SER 3.2 2.2 - - - -
112W LEU* 3.3 24.4 + - + +
115W LEU* 5.0 3.8 - - - +
139W VAL* 4.6 15.8 - - + +
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Residues in contact with ALA 110 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106W LEU 4.5 0.4 + - - -
107W ASP 3.0 14.5 + - - +
109W LEU* 1.3 78.5 - - - +
111W SER* 1.3 61.0 - - - +
112W LEU 3.4 4.7 + - - +
113W LYS* 4.8 1.6 + - - -
138W LYS* 3.1 30.3 - - + +
139W VAL* 4.6 5.5 - - - +
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Residues in contact with SER 111 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81W GLU 5.0 9.9 - - - -
83W LEU* 6.5 0.4 - - - -
84W ASP* 3.0 28.2 - - - +
108W PRO* 3.6 12.9 + - - -
109W LEU 3.2 1.2 - - - -
110W ALA* 1.3 78.9 - - - +
112W LEU* 1.3 55.3 + - - +
113W LYS* 3.2 8.2 + - - +
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Residues in contact with LEU 112 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83W LEU* 5.8 5.8 - - + -
84W ASP* 4.4 11.2 - - + +
87W LEU 5.6 2.5 - - - +
88W PRO 5.9 0.2 - - - -
90W LEU* 5.0 13.7 - - + +
108W PRO 4.6 1.0 + - - +
109W LEU* 3.3 21.7 + - + +
110W ALA 3.3 3.3 - - - +
111W SER* 1.3 72.4 - - - +
113W LYS* 1.3 64.9 + - - +
114W SER 3.4 2.5 - - - -
115W LEU* 3.2 29.7 + - + +
141W GLN* 4.5 6.1 - - - +
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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