Contacts of the helix formed by residues 110 - 128 (chain A) in PDB entry 4WNF
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A LEU* 5.2 0.8 - - - +
105A LEU* 3.0 32.1 + - + +
108A LEU* 3.7 26.7 - - - +
109A GLY* 1.3 81.0 - - - +
111A PHE* 1.3 63.7 + - - +
112A ASP 3.3 2.6 + - - -
113A GLU* 3.5 10.4 + - + +
114A ALA* 3.0 22.0 + - - +
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Residues in contact with PHE 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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106A LYS* 3.7 29.8 - - + -
109A GLY* 3.4 23.5 + - - -
110A ASN* 1.3 75.7 - - - +
112A ASP* 1.3 62.5 + - - +
114A ALA* 3.1 6.2 + - - +
115A ILE* 2.7 38.9 + - - +
144A VAL* 3.9 8.7 - - + +
147A ALA* 3.7 28.9 - - + -
148A LYS* 3.6 37.9 - - + -
151A SER* 3.3 31.2 - - - -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASN 3.3 1.0 - - - -
111A PHE* 1.3 83.8 - - - +
113A GLU* 1.3 61.5 + - - +
115A ILE* 3.3 10.9 + - - +
116A VAL* 3.3 23.5 + - - +
148A LYS* 4.1 21.3 - - - +
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Residues in contact with GLU 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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101A LEU* 5.5 2.6 - - - +
105A LEU* 4.0 29.4 - - + +
110A ASN* 3.5 11.2 + - + +
111A PHE 3.4 0.2 - - - -
112A ASP* 1.3 76.2 - - - +
114A ALA* 1.3 66.3 + - - +
116A VAL* 3.2 12.2 + - + +
117A CYS* 2.9 29.8 + - - -
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Residues in contact with ALA 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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102A GLY* 3.4 26.2 - - - +
105A LEU* 3.7 12.6 - - + +
106A LYS* 3.8 10.3 - - + +
110A ASN 3.0 15.6 + - - +
111A PHE* 3.2 13.2 - - - +
113A GLU* 1.3 76.0 - - - +
115A ILE* 1.3 57.4 + - - +
117A CYS* 3.0 1.9 + - - -
118A CYS* 2.8 35.5 + - - -
144A VAL* 4.2 9.4 - - + -
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Residues in contact with ILE 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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111A PHE 2.7 28.1 + - - +
112A ASP* 3.5 13.0 - - - +
113A GLU 3.3 0.2 - - - -
114A ALA* 1.3 70.4 - - - +
116A VAL* 1.3 61.1 + - + +
118A CYS* 3.7 0.4 - - - -
119A GLN* 2.7 38.6 + - + +
141A LEU* 3.9 9.3 - - + +
144A VAL* 3.5 22.2 - - + -
145A TYR* 3.5 47.3 - - + +
148A LYS* 4.4 18.2 - - + +
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Residues in contact with VAL 116 (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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112A ASP 3.4 14.8 - - - +
113A GLU* 3.2 14.3 + - + +
115A ILE* 1.3 80.0 - - + +
117A CYS* 1.3 60.9 + - - +
119A GLN* 3.3 7.4 + - + +
120A ARG* 3.0 33.4 + - + +
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Residues in contact with CYS 117 (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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82A LEU* 5.4 4.0 - - - -
98A SER* 3.3 37.0 - - - +
101A LEU* 4.1 20.0 - - - -
102A GLY* 3.5 17.0 - - - -
105A LEU* 3.9 17.7 - - - -
113A GLU* 2.9 25.0 + - - +
114A ALA 3.0 6.9 + - - +
116A VAL* 1.3 76.3 - - - +
118A CYS* 1.3 63.5 + - - +
120A ARG* 3.3 5.9 + - - +
121A HIS 3.3 6.8 + - - -
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Residues in contact with CYS 118 (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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98A SER 4.9 1.1 - - - -
99A GLY* 4.5 4.3 - - - -
102A GLY* 3.7 25.4 - - - -
103A ASN* 3.9 14.4 - - - -
114A ALA 2.8 21.6 + - - +
117A CYS* 1.3 69.5 - - - +
119A GLN* 1.3 65.6 + - - +
121A HIS* 3.1 10.6 + - - +
122A LEU* 3.0 21.3 + - - +
137A ALA* 4.3 2.6 - - - +
140A ASN* 4.2 9.6 - - + +
141A LEU* 3.3 31.3 - - + +
144A VAL* 4.0 17.0 - - - -
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Residues in contact with GLN 119 (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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115A ILE* 2.7 29.5 + - + +
116A VAL* 3.5 8.7 - - + +
118A CYS* 1.3 72.0 - - - +
120A ARG* 1.3 62.7 + - - +
122A LEU* 3.2 20.1 + - - +
123A ASP* 2.7 59.2 + - - +
126A ARG* 5.2 1.6 - - - +
141A LEU* 3.8 11.9 - - + +
177A PHE* 5.5 5.5 - - - -
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Residues in contact with ARG 120 (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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86A ARG* 3.4 28.2 - - - +
91A GLN* 5.4 3.8 - - - +
94A GLU* 3.2 23.5 + - - -
98A SER* 3.6 14.1 - - - +
116A VAL* 3.0 20.5 + - + +
117A CYS* 3.4 11.7 - - - +
118A CYS 3.2 0.2 - - - -
119A GLN* 1.3 73.4 - - - +
121A HIS* 1.3 66.7 + - - +
123A ASP* 3.8 7.2 - - - +
124A ILE* 3.0 52.7 + - + +
127A GLU* 5.2 5.1 + - - -
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Residues in contact with HIS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA* 3.3 35.8 - - + +
96A LYS* 4.9 1.0 - - - +
98A SER* 4.1 0.2 - - - -
99A GLY* 3.5 16.9 - - - +
117A CYS 3.3 8.8 + - - +
118A CYS* 3.2 11.3 - - - +
120A ARG* 1.3 79.7 - - - +
122A LEU* 1.3 60.3 + - - +
124A ILE* 3.9 1.4 - - - +
125A SER* 2.7 43.0 + - - -
133A GLY* 3.6 13.7 + - - -
137A ALA* 3.5 25.1 - - + +
140A ASN* 3.9 8.7 + - - -
1003B GLU* 3.7 41.0 - - + +
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Residues in contact with LEU 122 (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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118A CYS 3.0 11.3 + - - +
119A GLN* 3.3 20.0 - - - +
121A HIS* 1.3 77.5 - - - +
123A ASP* 1.3 61.0 + - - +
125A SER* 3.0 3.6 + - - -
126A ARG* 2.8 70.7 + - - +
134A GLU* 3.6 32.1 - - + +
137A ALA* 3.7 11.3 - - + +
138A LEU* 3.9 13.7 - - + -
141A LEU* 3.7 22.7 - - + -
177A PHE* 5.0 4.0 - - + -
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Residues in contact with ASP 123 (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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119A GLN* 2.7 45.6 + - - +
120A ARG* 3.8 7.6 - - - +
122A LEU* 1.3 78.5 - - - +
124A ILE* 1.3 58.5 + - + +
126A ARG* 3.4 13.4 + - - +
127A GLU* 2.9 38.3 + - - +
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Residues in contact with ILE 124 (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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91A GLN* 3.5 37.7 - - + +
94A GLU* 3.6 41.5 - - + +
95A ALA* 3.6 24.2 - - + +
120A ARG* 3.0 38.6 + - - +
123A ASP* 1.3 76.7 - - + +
125A SER* 1.3 57.9 + - - +
127A GLU* 3.3 11.4 + - + +
128A LEU* 2.9 42.9 + - + +
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Residues in contact with SER 125 (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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92A LEU* 5.7 2.5 - - - +
95A ALA* 4.3 5.2 - - - +
121A HIS* 2.7 38.1 + - - -
122A LEU 3.5 4.0 - - - -
124A ILE* 1.3 76.2 - - - +
126A ARG* 1.3 58.1 + - - +
128A LEU* 3.6 3.3 + - - -
129A ASN 3.0 6.9 + - - -
130A ASP* 2.7 43.1 + - - +
133A GLY* 3.8 7.6 - - - -
134A GLU* 3.6 28.3 - - - -
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Residues in contact with ARG 126 (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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119A GLN* 5.2 1.4 - - - +
122A LEU* 2.8 50.0 + - - +
123A ASP* 3.6 16.8 + - - +
125A SER* 1.3 73.1 - - - +
127A GLU* 1.3 68.6 + - - +
129A ASN* 2.7 22.8 + - - +
134A GLU* 3.0 36.2 + - - +
138A LEU* 4.1 3.4 - - - +
180A GLU* 3.4 23.4 + - - -
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Residues in contact with GLU 127 (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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91A GLN* 3.9 22.9 + - - +
120A ARG* 5.2 4.9 + - - -
123A ASP* 2.9 27.5 + - + +
124A ILE* 3.4 19.0 - - + +
126A ARG* 1.3 75.7 - - - +
128A LEU* 1.3 61.7 + - + +
129A ASN* 3.1 6.2 + - - +
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Residues in contact with LEU 128 (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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91A GLN* 3.9 24.2 - - + +
92A LEU* 4.0 36.1 - - + +
95A ALA* 5.6 0.2 - - + -
124A ILE* 2.9 39.5 + - + +
125A SER* 4.1 5.8 - - - +
127A GLU* 1.3 73.4 - - + +
129A ASN* 1.3 71.8 + - - +
130A ASP* 3.4 8.1 + - + +
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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