Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 2A79
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 VAL 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.1 27.4 - - + -
48A ARG 4.1 9.2 - - - +
49A VAL* 4.3 7.9 - - + -
82A ASN* 2.6 42.4 + - - +
83A LEU* 3.5 17.4 - - + +
84A PHE 3.1 22.5 + - - -
112A SER 5.3 0.7 - - - +
113A LEU* 1.3 79.4 - - - +
115A ILE* 1.3 58.8 + - - +
116A THR* 4.6 5.2 - - + -
153A ASP* 3.1 21.5 - - + +
154A VAL* 5.0 0.2 - - + -
241A MET* 6.1 0.4 - - + -
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Residues in contact with ILE 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 PHE* 3.5 29.4 - - + +
86A THR* 5.3 0.2 - - + -
99A LEU* 4.3 17.0 - - + -
103A ILE* 3.8 27.8 - - + -
110A ARG* 4.1 25.8 - - - +
113A LEU* 4.0 15.0 - - + -
114A VAL* 1.3 77.1 - - - +
116A THR* 1.3 71.0 + - - +
147A LEU* 4.5 7.6 - - + -
149A LEU* 4.2 16.2 - - + -
152A VAL* 3.6 9.8 - - + +
153A ASP* 2.8 35.1 + - - +
154A VAL 3.4 4.0 + - - -
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Residues in contact with THR 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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83A LEU* 3.8 23.2 - - + +
84A PHE 2.7 10.3 + - - +
85A ASP* 2.7 34.8 + - - +
86A THR* 2.9 26.5 + - - +
114A VAL* 4.4 4.0 - - + +
115A ILE* 1.3 84.0 - - - +
117A THR* 1.3 63.2 + - - +
152A VAL* 4.8 0.4 - - - -
154A VAL* 3.2 33.2 - - + -
156A PHE* 3.6 15.9 - - + -
214A GLN* 4.1 1.2 + - - -
241A MET* 4.5 4.4 - - + -
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Residues in contact with THR 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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86A THR* 3.3 14.4 - - - +
87A ALA* 3.3 10.2 - - - -
96A GLU* 2.8 27.1 + - - +
116A THR* 1.3 77.6 - - - +
118A LYS* 1.3 68.2 + - - +
119A ILE* 4.9 1.8 - - + -
140A LEU* 4.1 19.5 - - + -
143A SER* 4.3 8.5 - - - +
147A LEU* 4.9 2.5 - - + -
152A VAL* 3.9 25.3 - - + +
154A VAL 3.2 3.5 + - - +
155A VAL* 3.4 6.4 - - + +
156A PHE* 2.9 23.4 + - - -
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Residues in contact with LYS 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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85A ASP* 2.7 35.3 + - - +
86A THR 3.0 22.4 + - - +
87A ALA* 3.5 7.0 - - + +
88A GLU* 3.2 27.0 + - - +
90A TYR* 2.6 31.4 + - - -
117A THR* 1.3 76.8 + - - +
119A ILE* 1.3 65.2 + - - +
156A PHE* 3.4 26.2 - - + +
158A ASN* 3.5 28.2 + - + +
188A SER* 5.1 0.4 - - - -
214A GLN* 3.7 10.8 - - - +
1001A NAP 3.5 24.4 - - - +
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Residues in contact with ILE 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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88A GLU* 3.5 16.2 - - - +
117A THR* 4.9 3.1 - - + +
118A LYS* 1.3 80.3 - - - +
120A PHE* 1.3 64.4 + - - +
130A GLY 4.6 2.9 - - - +
131A LEU* 3.8 5.1 - - + +
135A HIS* 3.8 26.7 - - + +
136A ILE* 4.4 15.7 - - + +
139A GLY 3.6 26.0 - - - +
140A LEU* 3.7 10.1 - - + +
143A SER* 3.7 18.4 - - - +
155A VAL* 4.0 22.4 - - + -
156A PHE 2.8 13.7 + - - +
157A ALA* 3.7 4.8 - - - -
158A ASN* 2.9 23.2 + - - -
173A MET* 5.8 2.5 - - + -
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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