Contacts of the strand formed by residues 112 - 120 (chain A) in PDB entry 3ARE
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 SER 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A CYS* 4.8 4.5 - - - -
105A GLU 3.3 18.4 - - - -
106A MET* 3.9 16.8 - - - -
107A TYR* 4.3 3.3 - - - -
110A ASN 3.6 4.8 + - - -
111A ALA* 1.3 77.7 - - - +
113A GLU* 1.3 59.9 + - - +
114A SER* 3.9 2.8 + - - -
169A PRO* 3.3 31.1 - - - +
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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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104A CYS* 3.5 1.7 - - - -
105A GLU* 3.1 38.2 + - + +
107A TYR* 4.1 21.3 + - + +
112A SER* 1.3 71.6 - - - +
114A SER* 1.3 78.1 + - - +
115A PHE* 4.2 11.1 - - - +
129A TRP* 3.8 23.4 - - - -
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Residues in contact with SER 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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103A GLY 3.4 8.0 + - - -
104A CYS* 3.3 18.2 - - - +
112A SER 3.9 4.0 + - - -
113A GLU* 1.3 91.4 + - - +
115A PHE* 1.3 63.2 + - - +
129A TRP* 4.6 7.6 - - - -
164A LEU* 2.7 47.2 + - - +
165A ASN* 5.5 1.1 - - - -
168A CYS* 4.3 0.7 - - - +
169A PRO* 4.5 3.5 - - - +
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Residues in contact with PHE 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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9A THR* 4.7 3.8 - - + -
10A PHE 3.8 17.0 - - - -
11A ARG* 4.3 21.5 - - + -
101A SER* 3.8 27.1 - - - -
102A ALA* 3.4 5.6 - - - -
103A GLY 2.9 57.6 + - - +
104A CYS* 3.7 10.3 - - - -
105A GLU* 4.4 17.5 - - + -
113A GLU* 4.2 13.7 - - - +
114A SER* 1.3 78.2 - - - +
116A LEU* 1.3 63.2 + - - +
117A HIS* 4.1 30.1 - + + +
128A PHE 5.5 1.8 - - - -
129A TRP* 6.0 2.7 - - + -
164A LEU* 3.7 10.1 - - - +
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Residues in contact with LEU 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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100A LEU* 4.1 15.3 - - + -
101A SER 3.4 3.8 - - - -
102A ALA* 3.7 20.0 - - + -
115A PHE* 1.3 75.4 - - - +
117A HIS* 1.3 62.2 + - - +
118A VAL* 4.0 12.3 - - + -
127A ARG* 3.3 7.3 - - - +
128A PHE* 3.1 38.1 + - + -
133A TRP* 3.7 29.6 - - + -
160A VAL* 3.9 26.9 - - + -
164A LEU* 4.2 12.3 - - + -
601A 4GH 4.6 20.0 - - + -
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Residues in contact with HIS 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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100A LEU* 3.5 4.9 - - - +
101A SER* 2.7 40.6 + - - +
115A PHE* 4.1 33.2 - + + +
116A LEU* 1.3 74.7 - - - +
118A VAL* 1.3 62.8 + - - +
124A TYR* 3.0 40.0 + + + -
126A VAL 3.8 1.6 - - - -
127A ARG* 3.7 13.5 - - + +
60B TRP* 3.9 20.3 - + + -
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Residues in contact with VAL 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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98A ILE* 4.4 5.6 - - + -
99A GLN 3.5 10.3 - - - +
100A LEU* 3.6 24.0 - - + -
116A LEU* 4.0 12.8 - - + -
117A HIS* 1.3 79.3 - - - +
119A ALA* 1.3 69.6 + - - +
124A TYR* 3.3 5.7 - - - -
125A VAL* 3.0 23.5 + - + +
126A VAL* 2.7 32.7 + - + +
133A TRP* 4.1 13.0 - - + -
601A 4GH 3.8 34.8 - - + -
60B TRP* 4.5 0.7 - - - -
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Residues in contact with ALA 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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97A GLU 4.0 0.3 - - - +
98A ILE* 3.6 9.4 - - - +
99A GLN* 3.0 36.7 + - + +
118A VAL* 1.3 76.2 - - - +
120A PHE* 1.3 60.4 + - - +
121A GLN 4.2 0.7 - - - -
122A GLY 4.3 2.2 - - - -
123A LYS 3.2 26.5 - - - +
124A TYR 3.7 1.1 - - - +
125A VAL* 4.4 0.7 - - - -
60B TRP* 3.7 35.4 - - + -
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Residues in contact with PHE 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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92A GLU* 3.9 17.5 - - + -
96A ILE* 3.6 40.2 - - + -
97A GLU 3.8 1.3 - - - -
98A ILE* 4.3 5.2 - - + -
119A ALA* 1.3 72.1 - - - +
121A GLN* 1.3 91.2 + - + +
122A GLY 3.2 0.7 + - - -
123A LYS* 2.8 22.4 + - - +
125A VAL* 3.7 21.9 - - + +
140A PRO* 6.2 1.1 - - + -
142A TRP* 3.5 36.8 - + - -
143A LEU* 5.4 2.7 - - + -
601A 4GH 4.1 40.2 - - + -
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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