Contacts of the helix formed by residues 114 - 123 (chain A) in PDB entry 3W31
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 114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASN 3.4 4.6 + - - -
113A GLU* 1.3 77.3 - - - +
115A TYR* 1.3 66.9 + - - +
116A SER* 4.0 5.6 - - - +
117A LYS* 3.1 41.7 - - + +
118A PHE* 2.9 28.6 + - - +
177A PRO 3.3 0.9 + - - -
178A ASP* 3.0 35.3 - - + -
179A ALA 3.2 9.5 + - - -
180A PHE* 4.6 4.3 - - - +
181A VAL* 3.9 2.2 - - - -
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Residues in contact with TYR 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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39A MET* 4.2 15.4 - - + +
114A THR* 1.3 79.0 + - - +
116A SER* 1.3 56.9 + - - +
118A PHE* 3.4 1.7 + - - +
119A ARG* 2.9 29.2 + - - +
167A PHE* 4.1 19.0 - + - -
168A ASN* 4.6 7.4 - - + -
169A LEU* 4.0 27.3 - - + +
171A ASP* 2.7 31.2 + - - -
175A LYS* 3.2 35.7 - - + +
176A SER 3.8 9.4 - - - +
177A PRO 3.5 10.8 - - - +
179A ALA* 2.9 27.4 + - + +
180A PHE 3.5 18.8 - - - -
181A VAL* 3.6 21.2 - - + -
182A ASP* 5.1 6.2 + - - -
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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
----------------------------------------------------------
39A MET* 3.6 20.9 - - - +
114A THR* 3.8 4.9 + - - -
115A TYR* 1.3 71.2 - - - +
117A LYS* 1.3 58.2 + - - +
118A PHE 3.0 5.2 - - - -
119A ARG* 3.8 3.0 - - - +
120A GLU* 2.9 39.4 + - - +
177A PRO* 2.6 34.8 + - - +
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Residues in contact with LYS 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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110A HIS* 5.6 3.0 + - - +
111A PRO 5.3 1.8 + - - -
112A ASN* 4.6 5.3 + - - +
113A GLU* 3.0 40.9 + - + +
114A THR* 3.1 43.0 + - + +
116A SER* 1.3 78.4 - - - +
118A PHE* 1.3 57.6 + - - +
120A GLU* 4.5 3.8 - - - +
121A ARG* 3.3 18.0 + - - +
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Residues in contact with PHE 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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107A ILE* 3.9 8.7 - - + -
108A VAL* 3.8 7.4 - - - -
109A SER* 3.3 36.3 - - - -
113A GLU* 3.1 22.9 - - + +
114A THR 2.9 15.7 + - - +
115A TYR 3.9 3.1 - - - +
117A LYS* 1.3 77.8 - - - +
119A ARG* 1.3 60.7 + - - +
120A GLU 3.3 1.6 - - - -
121A ARG* 3.8 12.1 - - - -
122A ILE* 2.9 66.5 + - + +
167A PHE* 4.4 8.7 - + + -
169A LEU* 4.4 5.8 - - + -
181A VAL* 4.0 19.5 - - + -
185A SER* 3.6 18.6 - - - -
187A VAL* 4.3 11.7 - - + -
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Residues in contact with ARG 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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38A ASP* 3.7 22.6 + - - +
39A MET* 3.6 37.2 - - - +
42A ASP* 2.7 32.0 + - - -
115A TYR 2.9 18.4 + - - +
116A SER* 3.2 5.1 + - - +
118A PHE* 1.3 77.1 - - - +
120A GLU* 1.3 71.5 + - - +
122A ILE* 3.4 3.0 + - - +
123A ALA* 3.0 28.3 + - - +
156A ILE 3.4 23.2 + - - -
158A PHE* 3.4 25.8 - - + -
167A PHE* 3.9 32.1 - - + +
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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 SER* 2.9 21.2 + - - +
117A LYS* 4.5 4.7 - - - +
119A ARG* 1.3 85.1 + - - +
121A ARG* 1.3 64.4 + - - +
122A ILE 3.0 1.3 - - - -
123A ALA* 2.9 25.8 + - - +
124A GLU* 3.7 15.2 - - - +
127A LEU* 5.9 1.9 - - - +
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Residues in contact with ARG 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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107A ILE* 3.6 27.4 - - - +
108A VAL 2.5 38.0 + - - +
109A SER 3.9 0.2 - - - +
110A HIS* 2.8 34.1 + - - -
113A GLU* 3.1 22.4 + - - +
117A LYS 3.3 15.0 + - - +
118A PHE* 3.5 8.6 + - + +
119A ARG 3.5 0.4 - - - -
120A GLU* 1.3 78.9 - - - +
122A ILE* 1.3 60.1 + - - +
124A GLU* 3.6 21.5 - - + +
125A ASN 5.0 0.2 + - - -
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Residues in contact with ILE 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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107A ILE* 3.7 29.8 - - + +
118A PHE* 2.9 60.9 + - + +
119A ARG* 3.7 4.9 - - - +
120A GLU 3.0 0.2 - - - -
121A ARG* 1.3 75.1 - - - +
123A ALA* 1.3 53.6 + - - +
124A GLU 2.7 18.0 + - - -
125A ASN* 3.5 9.2 + - - +
126A ILE* 3.7 11.6 - - + +
138A ILE* 5.5 3.6 - - + -
158A PHE* 4.3 19.7 - - + -
167A PHE* 3.9 18.4 - - + -
187A VAL* 3.5 24.9 - - + -
189A VAL* 4.8 4.9 - - + -
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Residues in contact with ALA 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 ARG* 3.0 15.6 + - - +
120A GLU* 2.9 18.6 + - - +
122A ILE* 1.3 74.2 - - - +
124A GLU* 1.3 68.5 + - - +
126A ILE* 3.8 15.5 - - - -
127A LEU* 3.1 28.2 + - + +
156A ILE* 3.8 24.2 - - + +
158A PHE* 4.3 5.6 - - + -
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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