Contacts of the helix formed by residues 104 - 115 (chain F) in PDB entry 1W4R
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 ASP 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F LEU* 3.8 16.8 - - + +
81F LEU* 2.9 28.5 + - - +
82F ARG* 2.8 38.4 + - - +
102F PHE* 3.8 3.6 - - - +
103F PRO* 1.3 71.9 - - + +
105F ILE* 1.3 65.0 + - - +
106F VAL 3.2 3.3 + - - -
107F GLU* 3.3 19.6 + - + +
108F PHE* 3.0 23.9 + - + +
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LEU* 3.7 22.7 - - + -
96F ILE* 4.0 9.4 - - + -
99F GLY* 3.8 31.6 - - - +
100F GLN* 5.9 0.7 - - - +
102F PHE* 3.2 19.1 + - + +
103F PRO 3.4 0.6 - - - +
104F ASP* 1.3 77.6 + - - +
106F VAL* 1.3 69.5 + - + +
108F PHE* 4.0 0.3 - - - +
109F CYS* 3.0 47.7 + - - -
121F VAL* 4.2 7.2 - - + -
135F ALA* 4.1 31.4 - - + +
136F ILE* 4.1 7.2 - - + +
139F LEU* 3.8 19.3 - - + -
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Residues in contact with VAL 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PRO 5.1 0.2 + - - -
104F ASP 3.3 1.0 - - - -
105F ILE* 1.3 82.1 - - + +
107F GLU* 1.3 79.1 + - - +
109F CYS* 4.2 0.3 - - - +
110F GLU* 3.1 26.8 + - + +
135F ALA* 3.9 14.1 - - + +
138F ASN* 3.5 39.3 - - + +
139F LEU* 4.1 10.4 - - + +
142F LEU* 3.7 22.4 - - + -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F PRO 3.9 5.5 - - - +
104F ASP* 3.4 29.3 - - + +
106F VAL* 1.3 85.6 + - + +
108F PHE* 1.3 58.3 + - - +
110F GLU* 4.2 2.7 - - - +
111F ALA* 3.0 31.4 + - - +
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Residues in contact with PHE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ILE* 4.1 14.6 - - + -
81F LEU* 3.5 46.2 - - + -
82F ARG* 4.6 1.3 - - - -
84F VAL 4.9 0.2 - - - -
85F ALA* 4.3 5.8 - - + -
88F ALA* 3.7 24.9 - - + -
94F ILE* 4.1 11.9 - - + -
96F ILE* 3.7 30.5 - - + -
104F ASP* 3.0 18.7 + - - +
107F GLU* 1.3 75.3 - - - +
109F CYS* 1.3 68.9 + - - +
111F ALA* 3.4 3.8 + - - +
112F MET* 2.9 62.8 + - + +
119F VAL* 4.9 1.8 - - + -
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Residues in contact with CYS 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.7 21.9 - - + +
96F ILE* 3.8 6.7 - - - -
105F ILE* 3.0 37.9 + - - +
108F PHE* 1.3 80.7 - - - +
110F GLU* 1.3 59.1 + - - +
112F MET* 4.0 0.2 - - - -
113F ALA* 2.9 32.4 + - - +
119F VAL* 3.8 17.3 - - + +
121F VAL* 3.8 29.4 - - - -
139F LEU* 3.8 11.9 - - + -
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Residues in contact with GLU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 3.8 3.3 - - - +
106F VAL* 3.1 18.9 + - + +
107F GLU* 4.2 2.2 - - - +
109F CYS* 1.3 76.0 - - - +
111F ALA* 1.3 59.4 + - - +
113F ALA* 4.0 0.4 - - - +
114F ASN* 2.8 58.9 + - - +
142F LEU* 3.7 25.7 - - + +
130G ARG* 2.6 38.4 + - - -
186G ARG* 3.0 21.0 + - - -
190G PHE* 3.6 3.3 - - - -
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU 3.0 20.3 + - - +
108F PHE* 3.8 5.2 - - - +
110F GLU* 1.3 76.9 - - - +
112F MET* 1.3 64.4 + - + +
114F ASN* 3.4 5.2 + - - +
115F ALA* 3.0 28.1 + - - +
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Residues in contact with MET 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ALA* 3.7 30.5 - - + +
88F ALA* 3.9 5.4 - - + -
89F LEU* 4.0 26.9 - - + -
94F ILE* 3.9 17.5 - - + -
108F PHE* 2.9 57.3 + - + +
111F ALA* 1.3 79.5 - - + +
113F ALA* 1.3 65.7 - - - +
115F ALA* 3.1 8.7 + - - -
116F GLY 3.2 0.5 + - - -
117F LYS* 3.0 35.6 + - + +
119F VAL* 3.7 17.5 - - + -
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F GLY* 3.3 15.9 - - - -
20F GLN 3.8 13.7 - - - +
21F ILE* 3.7 15.0 - - + -
109F CYS 2.9 19.2 + - - +
110F GLU 4.0 0.2 - - - +
112F MET* 1.3 76.4 - - - +
114F ASN* 1.3 59.3 + - - +
116F GLY* 3.0 15.2 + - - -
117F LYS 3.5 10.8 - - - -
119F VAL* 4.0 1.0 - - + +
186G ARG* 3.5 31.6 - - - +
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Residues in contact with ASN 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F GLU* 2.8 47.4 + - - +
111F ALA* 3.7 5.3 - - - +
113F ALA* 1.3 76.4 - - - +
115F ALA* 1.3 55.8 + - - +
116F GLY 3.3 1.9 + - - -
186G ARG* 2.9 28.6 + - - +
187G LEU* 6.0 1.9 - - - +
190G PHE* 3.5 23.9 - - - -
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 5.2 3.0 + - - -
89F LEU* 5.0 10.1 - - + -
111F ALA 3.0 16.6 + - - +
112F MET* 3.1 8.7 + - - +
114F ASN* 1.3 76.0 - - - +
116F GLY* 1.3 56.1 + - - +
117F LYS* 3.5 19.4 + - + +
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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