Contacts of the helix formed by residues 111 - 123 (chain A) in PDB entry 5E6J
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TRP* 3.9 31.1 - - + -
105A ILE* 3.1 24.7 - - + +
106A LYS 2.8 23.2 + - - -
107A TRP* 3.5 14.0 - - - -
108A ALA* 3.0 30.1 + - - +
109A ASP 4.0 0.9 - - - -
110A ASN* 1.3 74.0 - - - +
112A CYS* 1.3 53.9 + - - +
113A TYR 3.2 3.1 - - - -
114A LEU* 3.1 12.8 + - + +
115A SER* 2.7 34.5 + - - -
76B AYE 4.2 0.8 - - - +
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Residues in contact with CYS 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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107A TRP* 3.7 16.8 - - + +
110A ASN 3.2 0.4 - - - -
111A ASN* 1.3 82.1 + - - +
113A TYR* 1.3 60.7 + - - +
115A SER* 3.4 8.3 + - - -
116A SER* 2.8 32.8 + - - -
274A TYR* 3.7 29.6 - - + +
75B GLY 3.6 4.0 - - - -
76B AYE 1.7 71.7 - - + +
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP 5.5 0.2 - - - -
110A ASN 3.2 24.5 - - - -
111A ASN* 4.7 0.4 - - - -
112A CYS* 1.3 76.0 - - - +
114A LEU* 1.3 88.5 + - + +
116A SER* 3.2 1.6 + - - -
117A VAL* 2.8 34.5 + - - +
153A LEU* 3.6 19.8 - - + +
158A LYS* 3.4 22.4 - - + +
159A THR 4.8 0.9 + - - -
162A GLU 3.4 21.7 + - - -
164A GLY* 3.8 24.5 - - - +
165A ASP 4.2 1.8 - - - -
166A VAL* 3.6 24.5 - - + +
169A THR* 3.7 24.9 - - - -
274A TYR* 3.9 12.3 - - + -
75B GLY 3.7 11.0 - - - -
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Residues in contact with LEU 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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94A TRP* 3.3 36.1 - - + -
105A ILE* 4.2 10.8 - - + -
109A ASP 5.9 0.4 - - - +
111A ASN* 3.1 13.2 + - + +
113A TYR* 1.3 107.6 - - + +
115A SER* 1.3 59.5 + - - +
117A VAL* 3.0 8.5 - - + +
118A LEU* 2.8 32.2 + - - +
149A CYS* 4.8 7.3 - - + +
152A ILE* 3.6 34.2 - - + +
153A LEU* 4.0 24.2 - - + -
169A THR* 4.9 0.2 - - + -
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Residues in contact with SER 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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103A THR 5.2 0.2 - - - +
104A SER* 3.1 25.3 + - - -
105A ILE* 3.6 31.1 + - - +
107A TRP* 5.7 0.9 - - - -
111A ASN* 2.7 21.0 + - - -
112A CYS* 3.5 9.4 - - - -
114A LEU* 1.3 72.2 - - - +
116A SER* 1.3 56.4 + - - +
118A LEU* 3.6 2.0 - - - +
119A LEU* 2.9 43.0 + - - +
288A GLY* 4.6 6.4 + - - -
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Residues in contact with SER 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 CYS 2.8 23.0 + - - -
113A TYR 3.4 5.4 - - - -
114A LEU 3.2 0.4 - - - -
115A SER* 1.3 73.8 - - - +
117A VAL* 1.3 60.5 + - - +
119A LEU* 3.5 7.1 + - - +
120A ALA* 2.8 32.2 + - - +
166A VAL* 3.7 15.7 - - - -
263A ASN* 3.4 21.5 + - - -
274A TYR* 3.6 16.5 - - - +
275A THR* 4.6 8.8 - - - -
276A HIS* 4.1 6.6 + - - +
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Residues in contact with VAL 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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113A TYR 2.8 21.9 + - - +
114A LEU* 3.0 25.4 - - - +
116A SER* 1.3 72.5 - - - +
118A LEU* 1.3 57.9 + - - +
120A ALA* 3.7 5.5 - - - +
121A LEU* 2.8 40.9 + - + +
152A ILE* 4.0 22.0 - - + -
166A VAL* 3.7 34.5 - - + +
169A THR* 4.1 21.5 - - + -
170A MET* 3.8 17.7 - - + -
173A LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 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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103A THR* 3.8 13.2 - - + +
104A SER 4.4 2.9 - - - +
105A ILE* 3.9 28.5 - - + -
114A LEU 2.8 18.2 + - - +
115A SER 3.6 3.8 - - - +
117A VAL* 1.3 74.9 - - + +
119A LEU* 1.3 65.4 + - - +
121A LEU* 3.2 6.4 + - - +
122A GLN* 2.9 47.0 + - + +
137A TYR* 5.3 2.7 - - + -
140A ALA* 4.0 14.6 - - + -
145A ALA* 4.0 20.2 - - + -
148A PHE* 3.7 32.5 - - + -
149A CYS* 4.7 3.8 - - - -
152A ILE* 5.6 1.3 - - + -
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Residues in contact with LEU 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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99A VAL 5.0 0.2 - - - +
102A LEU* 3.9 18.4 - - + +
103A THR 3.4 24.2 - - - +
104A SER* 4.0 6.7 - - - +
115A SER* 2.9 40.9 + - - +
116A SER 3.8 2.0 - - - +
118A LEU* 1.3 75.7 - - - +
120A ALA* 1.3 64.1 + - - +
122A GLN* 3.5 12.2 + - - +
123A GLN* 3.3 22.6 + - - +
276A HIS* 3.6 33.0 - - + -
286A ILE* 3.6 42.6 - - + +
288A GLY 5.9 0.2 - - - +
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Residues in contact with ALA 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 SER 2.8 20.0 + - - +
117A VAL* 3.7 7.2 - - - +
119A LEU* 1.3 77.8 - - - +
121A LEU* 1.3 62.5 + - - +
123A GLN* 3.0 15.1 + - - +
124A LEU* 3.3 17.5 + - + +
166A VAL* 6.2 0.4 - - + -
170A MET* 4.9 3.6 - - - -
261A CYS* 4.4 5.2 - - - -
263A ASN* 4.8 2.0 - - - +
276A HIS* 3.8 13.8 - - + -
305A PHE* 3.9 34.1 - - + -
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Residues in contact with LEU 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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117A VAL* 2.8 31.4 + - + +
118A LEU* 3.2 4.0 + - - +
120A ALA* 1.3 73.0 - - - +
122A GLN* 1.3 57.6 + - - +
124A LEU* 3.1 24.0 + - + +
126A VAL* 4.1 18.7 - - + +
128A PHE* 4.0 17.7 - - + -
137A TYR* 2.5 30.1 + - + -
148A PHE* 3.9 19.7 - - + -
152A ILE* 5.0 0.2 - - + -
170A MET* 4.3 24.2 - - + -
173A LEU* 3.4 31.9 - - + -
174A LEU* 4.8 7.6 - - + -
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Residues in contact with GLN 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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102A LEU* 3.6 25.8 - - + +
103A THR* 2.5 64.4 + - - +
118A LEU* 2.9 37.3 + - + +
119A LEU* 3.7 5.7 - - - +
120A ALA 3.2 0.2 - - - -
121A LEU* 1.3 75.8 - - - +
123A GLN* 1.3 59.3 + - - +
124A LEU 3.4 1.0 + - - +
137A TYR* 3.5 8.7 + - + -
141A ARG* 3.2 50.8 + - + +
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Residues in contact with GLN 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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102A LEU* 3.3 30.4 - - + +
119A LEU 3.3 12.0 + - - +
120A ALA 3.0 8.5 + - - +
122A GLN* 1.3 77.1 - - - +
124A LEU* 1.3 61.0 + - - +
125A GLU 4.2 0.3 + - - -
260A LEU* 3.5 30.4 - - + +
261A CYS* 3.5 19.9 - - - +
276A HIS* 2.9 31.9 + - - -
278A THR* 2.5 29.0 + - - -
307A LYS* 5.0 5.9 + - - -
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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