Contacts of the helix formed by residues 110 - 119 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASP* 1.3 69.8 - - + +
111B PHE* 1.3 63.5 + - - +
112B TYR 3.2 0.3 + - - -
113B ALA* 2.8 20.6 + - + +
114B ALA* 3.0 8.7 + - + +
117B MET* 6.5 0.2 - - - -
138B THR* 4.2 1.2 - - - +
139B SER 3.9 13.5 - - - +
140B ASN* 4.3 8.1 - - + -
141B TYR* 3.6 25.9 - - + -
144B ARG* 3.9 2.7 - - - +
603B 0KX 3.2 35.5 + - - -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET* 3.9 24.7 - - + -
109B ASP 2.6 13.9 + - - -
110B ALA* 1.3 68.0 - - - +
112B TYR* 1.3 82.6 + + - +
114B ALA* 2.8 15.2 + - - +
115B VAL* 2.9 23.3 + - + +
174B TYR* 3.8 32.1 - - + -
177B VAL* 3.8 26.7 - - + -
178B SER* 4.5 2.0 - - - -
181B VAL* 6.0 0.4 - - + -
197B LEU* 3.8 28.9 - - + -
198B ASP* 3.3 41.3 - - + +
307B LEU* 4.4 3.8 - - + -
603B 0KX 3.5 10.8 + - - +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA 3.2 1.4 + - - -
111B PHE* 1.3 100.9 - + - +
113B ALA* 1.3 58.3 + - - +
115B VAL* 3.3 3.5 + - - +
116B GLU* 3.0 31.2 + - - +
130B VAL* 3.7 15.5 - - + -
137B SER* 3.5 35.7 - - - -
138B THR* 3.6 10.5 - - + -
169B PRO* 5.1 0.9 - - + -
171B PHE* 3.9 11.3 - + - -
174B TYR* 3.7 47.9 - + + -
197B LEU* 4.7 7.4 - - + +
603B 0KX 3.9 29.0 + - + -
5T VKJ 3.6 33.5 + + - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 2.8 11.2 + - + +
112B TYR* 1.3 76.8 - - - +
114B ALA* 1.3 60.6 + - - +
116B GLU* 3.3 2.3 + - - +
117B MET* 2.9 35.2 + - - +
128B ILE* 3.7 19.1 - - + +
130B VAL* 3.7 13.9 - - + +
138B THR* 3.9 4.0 - - + +
139B SER* 4.0 6.1 - - - -
140B ASN* 3.9 27.4 - - + +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 6.2 0.2 - - + -
109B ASP 3.4 22.4 - - - +
110B ALA* 3.0 8.1 + - + +
111B PHE* 2.8 10.4 + - - +
113B ALA* 1.3 77.2 - - - +
115B VAL* 1.3 56.8 + - - +
117B MET* 3.1 11.1 + - - +
118B ARG* 2.9 24.6 + - - +
307B LEU* 3.5 27.8 - - + +
308B THR 6.0 0.9 - - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 2.9 31.0 + - + +
112B TYR 3.6 6.7 - - - +
114B ALA* 1.3 74.8 - - - +
116B GLU* 1.3 64.2 + - - +
117B MET 3.2 0.7 + - - -
118B ARG* 3.3 20.3 + - - +
119B ASP* 3.3 28.5 + - - +
173B LYS* 4.0 17.9 - - + +
174B TYR* 4.0 25.8 - - + -
177B VAL* 4.4 8.5 - - + -
307B LEU* 3.6 29.6 - - + -
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Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A SER* 2.6 29.8 + - - -
112B TYR 3.0 19.3 + - - +
113B ALA* 3.7 7.6 - - - +
114B ALA 3.3 0.2 - - - -
115B VAL* 1.3 77.6 - - - +
117B MET* 1.3 60.6 + - - +
119B ASP 3.8 1.5 + - - +
120B ASN* 3.4 18.4 + - - +
123B LEU* 3.6 14.6 - - + +
128B ILE* 4.5 2.9 - - + -
130B VAL* 3.8 11.9 - - + -
167B VAL* 3.9 31.0 - - + +
168B PRO 4.5 0.4 - - - +
170B ASN* 2.9 22.9 + - - +
173B LYS* 4.7 2.6 + - - -
174B TYR* 2.9 29.0 + - - +
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Residues in contact with MET 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 6.5 0.7 - - - -
113B ALA 2.9 22.7 + - - +
114B ALA* 3.6 8.7 - - - +
115B VAL 3.1 0.2 - - - -
116B GLU* 1.3 74.6 - - - +
118B ARG* 1.3 66.9 + - - +
119B ASP 3.2 0.6 + - - -
120B ASN 3.5 19.5 + - - +
121B PRO* 3.8 7.8 - - - +
123B LEU* 4.5 13.2 - - + +
124B LYS* 3.3 38.5 - - + +
128B ILE* 3.9 13.0 - - + -
140B ASN* 4.0 34.1 - - + +
142B HIS* 6.0 1.3 - - - +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ILE* 6.1 0.4 - - - +
427A LYS* 4.2 14.5 - - - +
430A GLU* 2.9 41.7 + - - -
114B ALA 2.9 12.4 + - - +
115B VAL* 3.5 14.5 + - - +
117B MET* 1.3 77.9 - - - +
119B ASP* 1.3 87.6 + - - +
120B ASN 3.5 0.4 + - - -
121B PRO* 4.5 9.2 - - - +
173B LYS* 4.6 3.4 - - - +
177B VAL* 3.8 18.1 - - - +
305B THR* 2.8 35.0 + - - +
306B THR* 3.8 24.5 - - + +
307B LEU* 4.2 14.1 - - + +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A SER* 4.7 4.5 - - - +
424A GLU* 3.2 48.7 + - + +
425A ILE* 5.4 1.6 - - - -
426A ASN* 5.6 6.6 + - - -
427A LYS* 5.4 1.6 + - - -
115B VAL* 3.3 12.0 + - - +
116B GLU 4.1 1.1 - - - +
117B MET 3.2 0.4 - - - -
118B ARG* 1.3 120.1 + - - +
120B ASN* 1.3 62.3 + - - +
121B PRO* 4.0 4.3 - - - +
173B LYS* 2.6 27.7 + - - +
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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