Contacts of the strand formed by residues 112 - 118 (chain A) in PDB entry 2HA7
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 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PRO* 3.3 23.1 - - + +
110A SER 2.9 16.1 + - - -
111A PRO* 1.3 71.0 - - - +
113A PRO* 1.3 81.4 - - + +
114A VAL* 3.5 0.3 - - - +
143A GLY 3.1 28.0 - - - +
144A ALA* 4.4 0.7 - - - -
145A VAL* 4.2 10.7 - - + +
191A GLY 2.9 12.3 + - - -
192A GLY* 3.3 5.0 - - - -
193A ASP* 2.7 29.1 + - - +
485A ARG* 6.3 0.2 - - - +
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Residues in contact with PRO 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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111A PRO 4.1 4.7 - - - +
112A THR* 1.3 95.9 - - + +
114A VAL* 1.3 59.9 + - - +
115A LEU* 4.1 1.5 + - - +
144A ALA* 4.3 4.7 - - - +
145A VAL 3.5 18.9 + - - -
193A ASP* 4.2 1.5 - - + +
196A SER* 3.6 28.0 - - - +
484A ALA* 4.9 7.0 - - + +
485A ARG* 4.0 45.8 - - + +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR 3.5 15.9 - - - +
113A PRO* 1.3 72.3 - - - +
115A LEU* 1.3 66.1 + - - +
116A ILE* 4.0 21.5 - - + -
145A VAL* 3.4 12.1 - - + +
147A VAL* 4.3 11.2 - - + -
183A VAL* 4.3 14.4 - - + -
187A ILE* 4.0 13.2 - - + -
192A GLY* 3.8 10.5 - - - -
193A ASP 3.6 21.8 - - - +
196A SER 2.8 13.2 + - - +
197A VAL* 3.4 7.3 - - + +
198A THR* 2.9 28.4 + - - -
484A ALA* 5.4 1.4 - - - +
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Residues in contact with LEU 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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113A PRO 4.1 1.5 + - - +
114A VAL* 1.3 74.2 - - - +
116A ILE* 1.3 61.6 + - - +
138A LEU* 4.7 16.2 - - + -
144A ALA* 4.0 19.1 - - + -
145A VAL 2.8 9.7 + - - +
146A LEU* 3.3 8.6 - - + +
147A VAL* 2.9 25.6 + - - +
198A THR* 3.5 13.5 - - + +
200A PHE* 4.0 34.8 - - + -
226A VAL* 6.0 0.7 - - + -
480A TRP* 4.8 11.9 - - + +
481A THR* 3.9 27.1 - - + -
484A ALA* 4.1 23.8 - - + -
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Residues in contact with ILE 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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114A VAL* 4.0 11.2 - - + -
115A LEU* 1.3 76.2 - - - +
117A TRP* 1.3 59.7 + - - +
118A ILE* 4.0 2.4 + - + +
147A VAL* 3.2 20.9 - - + +
149A MET* 3.7 29.2 - - + -
179A ALA 6.4 0.2 - - - -
180A LEU* 3.9 22.9 - - + -
183A VAL* 4.0 25.6 - - + -
197A VAL* 3.3 30.1 - - + -
198A THR 2.9 9.7 + - - +
199A LEU* 3.5 11.5 - - + +
200A PHE* 2.8 34.1 + - - +
221A LEU 5.4 0.4 - - - +
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Residues in contact with TRP 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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116A ILE* 1.3 72.9 - - - +
118A ILE* 1.3 71.2 + - - +
119A TYR* 3.7 18.5 + + + +
120A GLY 5.2 0.2 - - - -
128A ALA* 5.4 0.7 - - - -
133A TYR* 3.2 58.7 - + + -
146A LEU* 4.5 4.0 - - + -
147A VAL 2.8 13.5 + - - +
148A SER* 3.7 29.7 - - - -
149A MET* 3.8 12.0 + - - +
200A PHE* 3.2 63.2 - + + -
201A GLY* 3.5 14.6 - - - -
202A GLU* 3.5 30.5 - - + -
228A GLN* 4.1 9.4 - - - -
451A ILE* 4.2 11.4 - - + -
455A PHE* 3.6 17.5 - + + -
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Residues in contact with ILE 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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116A ILE* 4.6 5.6 - - + +
117A TRP* 1.3 81.0 - - - +
119A TYR* 1.3 68.0 + - - +
149A MET* 4.2 18.8 - - + -
151A TYR* 3.7 23.8 - - + -
176A GLN* 3.8 28.5 - - + +
180A LEU* 5.2 1.6 - - + -
199A LEU* 5.0 12.1 - - + -
200A PHE 2.9 13.4 + - - +
201A GLY* 3.3 13.2 - - - -
202A GLU 3.8 1.6 + - - -
205A GLY* 3.1 25.3 - - - +
208A SER* 4.1 3.8 - - - -
209A VAL* 4.2 18.4 - - + -
212A HIS* 4.3 15.9 - - + +
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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