Contacts of the helix formed by residues 110 - 119 (chain A) in PDB entry 4U7C
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 ALA 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ASP* 1.3 69.0 - - + +
111A PHE* 1.3 64.4 + - - +
112A TYR 3.2 1.1 + - - -
113A ALA* 2.9 19.6 + - + +
114A ALA* 3.0 8.1 + - + +
117A MET* 6.5 0.4 - - - -
138A THR* 4.3 1.6 - - - +
139A SER 3.9 16.8 - - - +
140A ASN* 4.4 7.9 - - + -
141A TYR* 3.7 23.7 - - + -
144A ARG* 3.8 1.3 - - - +
602A 0KX 3.3 35.1 + - - -
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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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108A MET* 3.9 24.7 - - + -
109A ASP 2.7 12.8 + - - -
110A ALA* 1.3 68.2 - - - +
112A TYR* 1.3 91.2 + + - +
114A ALA* 2.8 15.1 + - + +
115A VAL* 2.9 24.0 + - + +
174A TYR* 3.7 26.9 - - + -
177A VAL* 3.8 25.4 - - + -
178A SER* 4.5 1.6 - - - -
181A VAL* 6.2 0.2 - - + -
197A LEU* 4.0 26.9 - - + -
198A ASP* 3.3 29.6 - - + +
307A LEU* 4.5 3.6 - - + -
602A 0KX 3.1 21.7 + - - +
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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
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110A ALA 3.2 1.6 + - - -
111A PHE* 1.3 102.1 - + - +
113A ALA* 1.3 57.3 - - - +
115A VAL* 3.3 3.8 + - - +
116A GLU* 2.9 31.7 + - - +
130A VAL* 3.7 15.7 - - + -
137A SER* 3.7 21.5 - - - -
138A THR* 3.6 11.9 - - + -
169A PRO* 5.1 0.4 - - + -
171A PHE* 3.9 14.4 - - - -
174A TYR* 3.6 47.3 - + + -
197A LEU* 4.4 6.7 - - + +
602A 0KX 3.5 36.5 + - + -
5D VKJ 2.9 34.2 + + - -
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Residues in contact with ALA 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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110A ALA* 2.9 10.5 + - + +
112A TYR* 1.3 76.1 - - - +
114A ALA* 1.3 59.5 + - - +
116A GLU* 3.3 2.5 + - - +
117A MET* 2.9 36.5 + - - +
128A ILE* 3.7 18.8 - - + +
130A VAL* 3.6 14.1 - - + +
138A THR* 3.8 4.0 - - + +
139A SER* 4.1 6.7 - - - -
140A ASN* 3.9 27.8 - - + +
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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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108A MET* 6.2 0.7 - - + -
109A ASP 3.4 21.8 - - - +
110A ALA* 3.0 8.9 + - + +
111A PHE* 2.8 10.4 + - - +
113A ALA* 1.3 78.0 - - - +
115A VAL* 1.3 56.7 + - + +
117A MET* 3.2 11.2 + - - +
118A ARG* 2.9 28.4 + - - +
307A LEU* 3.5 23.5 - - + +
308A THR 5.9 1.3 - - - +
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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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111A PHE* 2.9 30.9 + - + +
112A TYR 3.5 7.0 - - - +
114A ALA* 1.3 76.8 - - - +
116A GLU* 1.3 62.5 + - - +
118A ARG* 3.2 20.3 + - - +
119A ASP* 3.4 19.5 + - - +
173A LYS* 3.9 28.7 - - + +
174A TYR* 4.0 23.3 - - + -
177A VAL* 4.5 8.1 - - + -
307A LEU* 3.7 28.7 - - + -
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Residues in contact with GLU 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 2.9 20.2 + - - +
113A ALA 3.7 6.1 - - - +
115A VAL* 1.3 76.6 - - - +
117A MET* 1.3 60.8 + - - +
119A ASP* 4.1 0.7 - - - +
120A ASN* 3.4 25.8 + - - +
123A LEU* 3.8 6.4 - - + +
128A ILE* 4.4 5.2 - - + -
130A VAL* 3.7 12.8 - - + -
167A VAL* 4.0 29.7 - - + +
168A PRO 4.5 0.7 - - - +
170A ASN* 3.1 20.5 + - - +
173A LYS* 4.5 1.8 + - - +
174A TYR* 2.7 31.4 + - - +
423B SER* 2.7 31.4 + - - -
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Residues in contact with MET 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 ALA* 6.5 0.2 - - - -
113A ALA 2.9 21.3 + - - +
114A ALA* 3.6 8.5 - - - +
115A VAL 3.1 0.2 - - - -
116A GLU* 1.3 76.4 - - - +
118A ARG* 1.3 67.0 + - - +
119A ASP 3.2 1.3 + - - -
120A ASN 3.3 21.4 + - - +
121A PRO* 3.9 5.7 - - - +
123A LEU* 4.6 8.1 - - + +
124A LYS* 3.3 48.6 - - + +
128A ILE* 4.0 13.0 - - + -
140A ASN* 3.8 34.3 - - + +
142A HIS* 6.5 0.2 - - + -
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Residues in contact with ARG 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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114A ALA 2.9 16.8 + - - +
115A VAL* 3.5 13.6 + - - +
117A MET* 1.3 77.9 - - - +
119A ASP* 1.3 87.8 + - - +
120A ASN 3.9 0.3 + - - -
121A PRO* 4.8 7.4 - - - +
173A LYS* 4.6 4.8 - - - +
177A VAL* 3.7 18.9 - - - +
305A THR* 2.9 34.9 + - - +
306A THR* 3.8 21.5 - - + +
307A LEU* 4.1 12.7 - - + +
424B GLU 5.4 0.2 + - - -
427B LYS* 4.1 14.9 - - - +
430B GLU* 2.8 42.1 + - - -
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Residues in contact with ASP 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 VAL 3.4 8.8 + - - +
116A GLU 4.1 1.1 - - - +
117A MET 3.2 0.2 - - - -
118A ARG* 1.3 119.2 + - - +
120A ASN* 1.3 61.9 + - - +
121A PRO* 4.0 5.6 - - - +
173A LYS* 2.8 27.7 + - - +
423B SER* 4.7 3.0 - - - +
424B GLU* 3.3 51.7 + - + +
425B ILE* 5.3 1.0 - - - -
426B ASN* 4.9 12.5 + - - +
427B LYS* 5.2 1.9 + - - -
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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