Contacts of the helix formed by residues 104 - 115 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A LEU* 3.6 17.8 - - + +
81A LEU* 2.9 28.4 + - - +
82A ARG* 2.8 39.1 + - - +
102A PHE* 4.0 3.5 - - - +
103A PRO* 1.3 77.1 - - - +
105A ILE* 1.3 62.9 - - - +
106A VAL 3.3 3.3 + - - -
107A GLU* 3.4 18.8 + - + +
108A PHE* 3.0 25.4 + - - +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU* 3.6 22.7 - - + -
96A ILE* 4.0 10.8 - - + -
99A GLY* 3.8 32.3 - - - +
100A GLN* 5.9 0.2 - - - -
102A PHE* 3.2 18.7 + - + +
103A PRO 3.3 0.6 - - - +
104A ASP* 1.3 77.1 + - - +
106A VAL* 1.3 71.0 + - + +
109A CYS* 3.0 44.8 + - - -
121A VAL* 4.2 5.6 - - + -
135A ALA* 4.1 29.8 - - + +
136A ILE* 4.2 7.6 - - + +
139A LEU* 3.9 18.8 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO 5.1 0.2 + - - -
104A ASP 3.3 0.4 - - - -
105A ILE* 1.3 80.1 - - + +
107A GLU* 1.3 79.1 + - + +
109A CYS* 3.9 0.5 - - - +
110A GLU* 3.0 28.3 + - + +
135A ALA* 4.0 15.2 - - + +
138A ASN* 3.6 32.5 - - + +
139A LEU* 3.9 16.9 - - + +
142A LEU* 3.6 22.9 - - + -
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO 4.0 4.5 - - - +
104A ASP* 3.4 29.6 - - + +
106A VAL* 1.3 86.5 + - + +
108A PHE* 1.3 63.5 + - - +
110A GLU* 4.1 2.9 - - - +
111A ALA* 3.0 27.6 + - - +
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Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 4.0 15.5 - - + -
81A LEU* 3.5 43.7 - - + -
82A ARG* 4.5 1.8 - - - -
84A VAL* 4.8 0.9 - - + -
85A ALA* 4.3 7.0 - - + -
88A ALA* 3.6 26.0 - - + -
94A ILE* 4.1 11.2 - - + -
96A ILE* 3.9 29.2 - - + -
104A ASP* 3.0 19.8 + - - +
107A GLU* 1.3 75.3 - - - +
109A CYS* 1.3 69.6 + - - +
111A ALA* 3.9 3.0 - - - +
112A MET* 3.0 61.4 + - + +
119A VAL* 4.9 1.8 - - + -
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Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.7 22.7 - - + +
96A ILE* 3.8 13.2 - - - -
105A ILE* 3.0 34.5 + - - +
108A PHE* 1.3 79.5 - - - +
110A GLU* 1.3 59.5 + - - +
112A MET* 4.0 0.5 - - - +
113A ALA* 2.9 32.1 + - - +
119A VAL* 3.7 26.0 - - + +
121A VAL* 3.8 20.0 - - - -
139A LEU* 3.9 11.2 - - + -
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.5 6.6 - - + +
106A VAL* 3.0 16.3 + - + +
107A GLU* 4.2 2.9 - - - +
109A CYS* 1.3 75.0 - - - +
111A ALA* 1.3 60.0 + - - +
113A ALA* 4.7 0.2 - - - -
114A ASN* 2.8 56.6 + - - +
142A LEU* 3.6 28.6 - - + +
130D ARG* 2.5 39.5 + - - -
186D ARG* 2.8 28.6 + - - -
190D PHE* 4.1 1.0 - - - -
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU 3.0 19.9 + - - +
108A PHE* 3.9 4.0 - - - +
110A GLU* 1.3 76.0 - - - +
112A MET* 1.3 64.4 + - + +
114A ASN* 3.4 5.3 + - - +
115A ALA* 3.0 29.1 + - - +
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA* 4.0 14.6 - - + +
88A ALA* 4.0 11.9 - - + -
89A LEU* 3.9 32.1 - - + -
94A ILE* 3.7 25.4 - - + -
108A PHE* 3.0 50.3 + - + +
111A ALA* 1.3 80.8 - - + +
113A ALA* 1.3 65.2 + - - +
115A ALA* 3.1 8.5 + - - -
116A GLY 3.2 0.5 + - - -
117A LYS* 2.9 34.9 + - + +
119A VAL* 3.7 18.6 - - + -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY* 3.2 16.6 + - - -
20A GLN 3.7 15.7 - - - +
21A ILE* 3.7 13.0 - - + -
109A CYS 2.9 19.3 + - - +
110A GLU 4.1 0.2 - - - +
112A MET* 1.3 76.1 - - - +
114A ASN* 1.3 60.5 + - - +
116A GLY 3.1 14.0 + - - -
117A LYS 3.3 11.7 - - - -
119A VAL* 4.0 1.5 - - + +
186D ARG* 3.6 31.0 - - - +
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Residues in contact with ASN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 2.8 44.5 + - - +
111A ALA* 3.7 5.3 - - - +
113A ALA* 1.3 78.3 - - - +
115A ALA* 1.3 56.4 + - - +
116A GLY 3.3 1.4 + - - -
186D ARG* 2.9 33.1 + - - +
187D LEU* 6.1 0.7 - - - +
190D PHE* 3.6 19.1 - - - -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 5.2 9.6 - - + -
111A ALA 3.0 17.2 + - - +
112A MET* 3.1 7.8 + - - +
114A ASN* 1.3 76.2 - - - +
116A GLY* 1.3 58.6 + - - +
117A LYS* 3.6 19.5 + - + +
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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