Contacts of the helix formed by residues 111 - 125 (chain A) in PDB entry 4WCX
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 THR 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS 3.6 2.9 + - - +
110A LEU* 1.3 76.0 - - - +
112A MET* 1.3 56.1 + - - +
113A GLU* 3.8 15.3 + - - +
114A GLU* 2.9 40.5 + - - +
115A VAL* 2.7 34.3 + - - +
145A TYR* 5.5 0.2 - - - -
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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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110A LEU 4.0 0.4 + - - -
111A THR* 1.3 73.0 - - - +
113A GLU* 1.3 70.0 + - - +
115A VAL* 3.5 10.4 - - - +
116A ARG* 2.8 38.7 + - + +
145A TYR* 4.3 13.0 - - + +
148A ASP* 3.0 52.0 - - + +
149A VAL* 3.4 11.4 - - + +
152A THR* 3.3 24.9 - - + +
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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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111A THR* 3.1 13.5 - - - +
112A MET* 1.3 90.9 + - - +
114A GLU* 1.3 58.6 + - + +
116A ARG* 3.4 11.2 + - - +
117A ARG* 3.0 25.7 + - - +
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Residues in contact with GLU 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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108A LYS* 3.7 22.5 + - - -
109A LYS 4.2 2.9 - - - +
110A LEU* 3.7 16.0 - - + -
111A THR* 2.9 41.1 + - - +
113A GLU* 1.3 77.5 - - + +
115A VAL* 1.3 55.1 + - - +
117A ARG* 3.2 8.5 + - - +
118A GLU* 2.8 41.3 + - + +
342A HIS* 5.6 9.9 - - + +
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Residues in contact with VAL 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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84A LEU* 4.9 4.3 - - + -
86A VAL* 5.1 1.8 - - + -
110A LEU* 3.5 28.9 - - + +
111A THR 2.7 24.7 + - - +
112A MET* 3.5 13.7 - - - +
114A GLU* 1.3 71.7 - - - +
116A ARG* 1.3 63.3 + - - +
118A GLU* 3.1 4.0 + - - +
119A VAL* 2.9 26.4 + - + +
149A VAL* 4.3 27.6 - - + +
152A THR* 3.8 19.7 - - + -
153A ILE* 4.2 23.1 - - + -
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Residues in contact with ARG 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 MET* 2.8 27.5 + - - +
113A GLU* 3.7 10.0 + - - +
115A VAL* 1.3 73.8 - - - +
117A ARG* 1.3 58.2 + - - +
119A VAL* 3.3 2.6 + - - +
120A GLU* 2.9 44.4 + - - +
152A THR* 3.4 25.3 + - + +
155A ASP* 3.7 34.9 + - - +
156A THR* 3.3 34.1 + - + +
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Residues in contact with ARG 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 GLU 3.0 15.7 + - - +
114A GLU* 3.5 11.7 - - - +
115A VAL 3.2 0.4 - - - -
116A ARG* 1.3 76.2 - - - +
118A GLU* 1.3 61.7 + - - +
120A GLU* 3.3 14.3 + - - +
121A ILE* 2.9 32.7 + - + +
342A HIS* 4.4 23.8 - - + +
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Residues in contact with GLU 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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84A LEU* 3.7 19.3 - - + +
85A TYR 5.2 0.5 - - - +
110A LEU* 3.7 21.0 - - + +
114A GLU* 2.8 21.8 + - + +
115A VAL* 3.4 8.7 - - - +
117A ARG* 1.3 72.7 - - - +
119A VAL* 1.3 63.3 + - - +
121A ILE* 3.1 10.3 + - - +
122A LEU* 3.0 26.4 + - - +
337A GLY 5.0 0.2 - - - +
339A GLY* 3.3 20.2 + - - -
340A GLY 3.4 1.2 + - - -
341A TYR* 3.0 35.0 + - + +
342A HIS* 2.8 36.4 + - - +
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Residues in contact with VAL 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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84A LEU* 4.4 6.1 - - + -
115A VAL* 2.9 25.5 + - + +
116A ARG* 3.7 4.7 - - - +
118A GLU* 1.3 77.0 - - - +
120A GLU* 1.3 51.2 + - - +
122A LEU* 3.2 8.4 + - - +
123A GLU* 2.7 56.9 + - - +
130A LEU* 4.4 7.6 - - + -
153A ILE* 3.9 35.0 - - + +
156A THR* 3.5 18.8 - - + +
163A ILE* 3.8 15.7 - - + -
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Residues in contact with GLU 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 ARG* 2.9 34.4 + - - +
117A ARG* 3.6 10.7 - - - +
118A GLU 3.3 0.2 - - - -
119A VAL* 1.3 68.3 - - - +
121A ILE* 1.3 67.3 + - + +
123A GLU* 3.8 6.9 - - - +
124A GLU* 2.9 31.7 + - - +
156A THR* 4.0 16.7 - - + +
157A LYS 5.0 3.6 - - - +
158A LEU* 4.0 27.8 - - + +
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Residues in contact with ILE 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 ARG* 2.9 29.3 + - + +
118A GLU* 3.1 11.4 + - - +
120A GLU* 1.3 76.1 - - + +
122A LEU* 1.3 57.1 + - - +
124A GLU* 3.3 8.6 + - + +
125A MET* 3.1 39.7 + - + +
341A TYR* 3.8 23.6 - - + +
342A HIS* 3.6 38.8 - - + +
344A GLU* 6.1 2.7 - - + -
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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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82A ALA* 3.8 10.3 - - + -
83A PRO 4.9 0.2 - - - +
84A LEU* 4.1 24.9 - - + -
118A GLU 3.0 18.7 + - - +
119A VAL* 3.4 8.1 - - - +
121A ILE* 1.3 75.1 - - - +
123A GLU* 1.3 64.5 + - - +
125A MET* 3.0 20.5 + - - +
127A HIS* 3.2 41.6 + - + +
130A LEU* 3.7 34.8 - - + -
163A ILE* 5.2 1.1 - - + -
341A TYR* 3.6 38.8 - - + -
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Residues in contact with GLU 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 VAL* 2.7 36.6 + - - +
120A GLU* 3.8 4.5 - - - +
122A LEU* 1.3 72.2 - - - +
124A GLU* 1.3 56.8 + - - +
126A GLY* 2.9 17.3 + - - -
127A HIS 4.0 8.2 - - - +
156A THR* 2.6 29.3 - - - +
157A LYS 3.7 1.6 - - - -
158A LEU* 3.3 33.3 + - + +
161A GLY* 3.5 10.3 - - - +
162A SER* 3.5 19.0 - - - +
163A ILE* 3.4 28.4 + - + +
421A TYR* 3.1 20.7 + - - -
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Residues in contact with GLU 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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120A GLU 2.9 26.2 + - - +
121A ILE* 3.5 9.2 - - + +
122A LEU 3.2 0.2 - - - -
123A GLU* 1.3 75.1 - - - +
125A MET* 1.3 58.5 + - - +
126A GLY 3.3 0.4 - - - -
158A LEU* 3.5 27.8 - - + +
159A LYS* 3.4 34.6 + - - +
421A TYR* 3.4 31.6 + - - +
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Residues in contact with MET 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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121A ILE* 3.1 24.0 + - + +
122A LEU* 3.0 26.8 + - + +
124A GLU* 1.3 78.2 - - - +
126A GLY* 1.3 55.9 + - - +
127A HIS* 3.6 18.8 + - + +
333A GLY* 3.6 28.9 - - - +
341A TYR* 4.4 10.3 - - - -
363A PRO* 3.4 42.1 - - + +
364A ASN* 5.8 0.9 + - - -
379A TYR* 4.9 0.3 + - - -
417A PHE* 3.7 15.1 - - - -
421A TYR* 4.5 3.6 - - - -
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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