Contacts of the strand formed by residues 237 - 244 (chain A) in PDB entry 2AVN
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 HIS 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.8 0.2 - - - -
25A TRP* 3.7 29.5 - + - -
28A TYR* 4.2 8.7 - - - -
111A ASP* 3.1 38.5 + - - +
139A THR* 5.1 4.5 - - - -
140A VAL 3.7 6.5 - - - +
141A ASP* 3.4 16.8 + - - -
142A ASN* 4.6 1.6 - - - -
200A GLY 3.8 0.2 - - - -
201A ILE* 2.9 43.7 + - + +
235A ALA* 3.6 7.8 - - - +
236A ASP* 1.3 102.8 + - - +
238A ILE* 1.3 67.9 + - - +
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Residues in contact with ILE 238 (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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138A ALA 4.0 0.2 - - - +
139A THR* 3.0 6.3 - - - -
140A VAL* 2.8 49.4 + - + +
142A ASN* 4.0 17.9 - - + +
187A LEU* 4.3 9.2 - - + -
198A ILE* 3.6 26.0 - - + -
199A ARG 3.7 6.3 - - - +
201A ILE* 4.6 0.7 - - - -
232A ILE* 3.4 29.4 - - + +
233A TRP* 3.5 46.0 - - + -
237A HIS* 1.3 81.9 - - - +
239A PHE* 1.3 62.9 + - - +
240A PHE* 4.3 0.6 + - + -
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Residues in contact with PHE 239 (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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32A ILE* 4.0 8.1 - - + -
35A PHE* 3.7 42.2 - + + -
36A LEU* 5.1 3.1 - - + -
39A TYR* 4.0 15.5 - + - -
109A LEU* 4.9 3.4 - - + -
137A ILE* 3.5 32.1 - - + -
138A ALA 3.2 14.6 - - - -
139A THR* 4.0 13.2 - - + -
197A ASP* 5.5 1.1 - - + -
198A ILE* 3.4 2.6 - - - +
199A ARG* 2.7 52.2 + - + +
201A ILE* 3.6 22.6 - - + +
237A HIS 4.2 0.6 + - - -
238A ILE* 1.3 73.4 - - - +
240A PHE* 1.3 65.5 + - - +
241A VAL* 3.6 24.5 - - + -
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Residues in contact with PHE 240 (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 LEU* 4.1 14.1 - - + -
123A PHE* 4.6 5.8 - + - -
136A LEU* 4.1 12.3 - - + -
137A ILE* 3.5 3.6 - - - +
138A ALA* 2.8 56.4 + - + -
140A VAL* 3.8 33.9 - - + -
182A PHE* 5.0 0.7 - + - -
187A LEU* 3.7 45.5 - - + -
195A THR* 5.6 0.2 - - + -
197A ASP 3.4 12.3 - - - +
198A ILE* 4.2 5.6 - - + -
238A ILE* 4.6 0.9 - - + -
239A PHE* 1.3 80.3 - - - +
241A VAL* 1.3 66.2 + - - +
242A LEU* 3.7 35.0 - - + -
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Residues in contact with VAL 241 (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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39A TYR* 4.0 29.8 - - + +
135A LEU* 4.1 20.6 - - + -
136A LEU 3.1 8.3 - - - +
137A ILE* 4.5 7.6 - - + -
195A THR 3.8 0.2 - - - -
196A VAL* 2.8 51.4 + - + -
197A ASP* 2.9 15.0 + - + +
239A PHE* 3.6 26.9 - - + -
240A PHE* 1.3 80.2 - - - +
242A LEU* 1.3 69.3 + - - +
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A PHE* 4.4 1.1 - - + -
134A GLY 3.7 0.3 - - - +
135A LEU* 3.1 8.1 - - - +
136A LEU* 2.9 49.8 + - + +
187A LEU* 5.2 2.7 - - + +
190A LEU* 3.6 28.5 - - + -
193A PHE* 3.5 39.3 - - + -
194A GLU 3.3 5.8 - - - +
195A THR* 3.7 28.5 - - + +
196A VAL* 4.2 2.7 - - - -
240A PHE* 3.7 23.6 - - + -
241A VAL* 1.3 82.8 - - - +
243A LYS* 1.3 60.4 + - - +
244A LYS 4.2 0.2 - - - -
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Residues in contact with LYS 243 (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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133A ASP* 3.8 43.5 - - - +
134A GLY 3.4 2.7 - - - -
135A LEU* 4.0 10.8 - - + -
193A PHE* 3.5 4.0 - - - -
194A GLU* 2.9 55.9 + - - +
196A VAL* 3.6 20.0 - - + -
242A LEU* 1.3 73.9 - - - +
244A LYS* 1.3 67.8 + - - +
245A LYS* 3.2 1.1 + - - -
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Residues in contact with LYS 244 (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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101A GLY* 5.3 0.8 - - - +
127A ARG* 2.8 55.6 + - + +
128A ARG* 3.9 7.3 + - - +
130A LEU* 2.7 33.2 + - + +
131A VAL 3.5 16.0 - - - +
132A PRO* 4.3 14.5 - - + +
133A ASP* 3.0 29.7 + - - +
134A GLY 2.9 17.0 + - - +
192A GLY 3.8 5.2 - - - -
193A PHE* 4.0 13.2 - - + -
243A LYS* 1.3 71.2 - - - +
245A LYS* 1.3 69.5 + - - +
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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