Contacts of the helix formed by residues 110 - 121 (chain A) in PDB entry 4WUR
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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93A TRP* 3.5 44.5 - - + -
104A LEU* 3.6 15.9 - - - +
105A LYS 3.4 18.5 + - - +
106A LEU* 3.5 9.9 - - - -
107A SER 2.9 33.3 + - - +
108A ASP 4.2 0.7 - - - +
109A ASN* 1.3 75.1 - - - +
111A SER* 1.3 67.8 + - - +
112A TYR* 3.1 11.2 - - - -
113A LEU* 2.9 18.1 + - + +
114A ASN* 3.3 8.1 + - - +
76B GLY* 3.6 1.2 + - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.9 0.9 - - - -
109A ASN 3.4 2.6 - - - -
110A ASN* 1.3 81.9 + - - +
112A TYR* 1.3 63.2 + - - +
114A ASN* 3.0 5.9 + - - +
115A ALA 3.0 18.4 + - - -
278A HIS* 3.3 29.4 - - - -
279A TYR* 3.1 26.8 + - - +
294A SER* 3.4 15.0 - - - -
76B GLY* 2.6 29.8 + - - -
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TRP* 5.5 0.3 - - - -
108A ASP 5.6 0.2 - - - -
109A ASN 3.2 24.9 - - - -
110A ASN* 4.0 8.5 - - - -
111A SER* 1.3 81.8 + - - +
113A LEU* 1.3 85.7 + - + +
115A ALA 3.3 1.6 + - - -
116A VAL* 3.0 29.5 + - - +
153A MET* 4.1 4.7 - - - -
158A CYS* 3.6 22.6 - - - +
159A THR 4.8 2.6 + - - -
162A ALA 4.1 8.4 + - - -
164A ASP* 3.3 46.4 - - + +
165A ASP 4.3 6.1 - - - -
166A ALA* 3.5 12.3 - - + +
169A LEU* 3.8 23.3 - - + -
279A TYR* 3.4 23.3 - - + -
75B GLY 3.4 9.6 - - - +
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Residues in contact with LEU 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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93A TRP* 3.2 40.2 - - + -
104A LEU* 3.7 9.9 - - + -
110A ASN* 2.9 11.5 + - + +
112A TYR* 1.3 108.9 - - + +
114A ASN* 1.3 64.5 + - - +
116A VAL* 2.9 4.5 + - + +
117A ILE* 2.7 45.0 + - + +
149A ILE* 4.4 7.2 - - + +
152A ILE* 4.4 7.9 - - + -
153A MET* 3.6 24.9 - - + -
169A LEU* 3.9 16.4 - - + -
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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
----------------------------------------------------------
103A SER* 2.4 27.1 + - - -
104A LEU* 2.9 42.1 + - + +
110A ASN 3.3 4.6 + - - +
111A SER* 3.0 10.1 + - - +
113A LEU* 1.3 78.2 - - - +
115A ALA* 1.3 62.1 + - - +
117A ILE* 4.8 2.0 - - - -
118A MET* 3.1 41.7 + - - +
279A TYR 5.1 2.6 + - - -
281A HIS* 4.1 6.7 - - - +
292A PHE 3.0 27.1 + - - -
294A SER* 3.5 15.2 + - - +
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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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111A SER 3.0 11.4 + - - +
112A TYR 3.6 8.3 - - - +
113A LEU 3.1 0.2 - - - -
114A ASN* 1.3 76.5 - - - +
116A VAL* 1.3 63.0 + - - +
118A MET 4.0 0.2 - - - -
119A THR* 2.7 32.0 + - - -
166A ALA* 4.3 7.9 - - + -
267A ASN* 3.7 28.6 - - + +
279A TYR* 4.1 17.0 - - + -
280A VAL 4.9 3.4 - - - +
281A HIS* 4.0 9.8 + - + -
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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 TYR 3.0 17.7 + - - +
113A LEU* 2.9 9.9 + - - +
115A ALA* 1.3 76.4 - - - +
117A ILE* 1.3 65.1 + - + +
119A THR* 3.1 3.2 + - - -
120A LEU* 2.9 48.2 + - + +
152A ILE* 4.7 9.0 - - + -
166A ALA* 3.4 27.6 - - - +
169A LEU* 4.1 21.5 - - + -
170A LEU* 3.9 29.5 - - + +
173A VAL* 4.8 1.8 - - + -
267A ASN* 5.7 0.2 - - - +
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Residues in contact with ILE 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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95A MET* 5.0 9.6 - - + -
102A ARG 5.4 1.8 - - - +
103A SER* 6.5 0.2 - - - -
104A LEU* 4.8 6.7 - - + +
113A LEU* 2.7 58.5 + - + +
114A ASN* 4.3 2.5 - - - +
116A VAL* 1.3 78.1 - - + +
118A MET* 1.3 67.8 + - + +
120A LEU* 3.3 7.0 + - + +
121A ASP* 2.9 30.2 + - - +
140A HIS* 3.6 34.1 - - + +
148A PHE* 4.9 12.3 - - + -
149A ILE* 4.7 22.2 - - + -
152A ILE* 4.9 6.5 - - + -
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Residues in contact with MET 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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101A VAL* 3.4 33.0 - - + -
102A ARG 3.8 14.6 - - - +
103A SER* 3.1 26.5 - - - -
104A LEU 5.2 0.2 - - - +
114A ASN* 3.1 28.3 + - - +
117A ILE* 1.3 82.7 - - + +
119A THR* 1.3 60.7 + - - +
121A ASP* 3.6 7.7 - - - +
122A LEU* 3.3 8.3 - - - +
281A HIS* 3.4 28.5 - - + -
283A ARG* 2.8 30.0 + - - +
292A PHE* 3.5 31.2 - - + -
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Residues in contact with THR 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 ALA 2.7 18.2 + - - -
116A VAL 3.4 8.5 - - - -
118A MET* 1.3 75.4 - - - +
120A LEU* 1.3 59.4 + - - +
122A LEU* 3.0 26.3 + - + +
123A LEU* 3.4 16.4 - - + +
170A LEU* 3.8 27.1 - - + -
245A LEU* 4.4 16.8 - - + -
267A ASN* 3.2 23.2 + - - +
281A HIS* 3.6 10.4 + - + -
309A ASP* 5.8 0.2 - - + -
311A LEU* 5.2 8.5 - - + -
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Residues in contact with LEU 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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116A VAL* 2.9 37.0 + - + +
117A ILE* 3.7 6.5 - - - +
119A THR* 1.3 71.7 - - - +
121A ASP* 1.3 61.4 + - - +
122A LEU 2.9 6.4 + - - -
123A LEU* 3.2 36.8 + - + +
126A ILE* 4.5 12.3 - - + +
128A PHE* 5.0 1.8 - - + -
137A PHE* 4.6 16.7 - - + -
140A HIS* 6.3 0.2 - - - +
148A PHE* 3.8 28.5 - - + -
152A ILE* 4.2 0.9 - - + -
170A LEU* 3.8 18.8 - - + -
173A VAL* 3.8 21.1 - - + -
174A LEU* 4.1 16.6 - - + -
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Residues in contact with ASP 121 (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 ARG* 4.1 17.0 + - - +
117A ILE* 2.9 30.0 + - - +
118A MET* 3.6 13.0 - - - +
119A THR 3.1 0.2 - - - -
120A LEU* 1.3 77.6 - - - +
122A LEU* 1.3 62.4 + - + +
123A LEU 5.3 1.1 - - - +
137A PHE* 5.2 2.9 - - - -
140A HIS* 2.9 30.3 + - - -
141A LYS* 5.5 2.4 - - - +
283A ARG* 4.2 8.2 + - - +
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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