Contacts of the strand formed by residues 240 - 246 (chain A) in PDB entry 4JVA
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 GLY 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.6 7.4 - - - +
173A VAL* 2.9 44.4 + - - +
194A ARG* 3.6 22.3 + - - -
195A GLY* 3.8 4.9 - - - -
197A PHE* 5.0 0.7 - - - -
238A SER 3.4 1.0 + - - -
239A PRO* 1.3 74.8 - - - +
241A ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 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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170A GLU* 4.8 7.0 - - + +
171A LYS 3.6 7.9 - - - +
172A LEU* 4.0 9.2 - - + +
173A VAL* 3.8 1.4 - - - +
193A ASP* 3.1 28.1 + - + -
194A ARG* 3.4 50.8 + - + +
240A GLY* 1.3 75.4 - - - +
242A LEU* 1.3 69.4 + - - +
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Residues in contact with LEU 242 (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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169A PHE 3.7 0.2 - - - +
170A GLU* 3.5 6.5 - - - +
171A LYS* 2.8 39.1 + - + +
173A VAL* 4.0 19.7 - - + -
179A VAL* 3.9 31.4 - - + -
190A TYR* 3.9 22.7 - - + -
191A VAL 3.5 15.7 - - - +
192A ILE* 3.7 24.2 - - + -
193A ASP 4.3 1.3 - - - +
197A PHE* 3.9 14.8 - - + -
219A PHE* 4.1 10.8 - - + -
241A ALA* 1.3 83.1 - - - +
243A TRP* 1.3 66.4 + - - +
244A GLY 3.9 0.4 - - - -
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Residues in contact with TRP 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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135A LYS* 4.1 19.5 - - + -
139A GLN* 3.5 35.2 - - + -
142A ARG* 3.4 14.8 - - - -
143A LEU* 3.8 28.8 - - + +
146A ALA* 3.8 20.6 - - + +
168A MET* 4.1 21.9 - - + +
169A PHE 3.3 17.0 - - - -
170A GLU* 3.6 37.2 - - + -
189A PHE* 3.8 0.5 - - - +
190A TYR* 3.6 3.3 - - - -
191A VAL* 2.9 41.2 + - + +
193A ASP* 2.6 43.0 + - + +
242A LEU* 1.3 72.7 - - - +
244A GLY* 1.3 61.8 + - - +
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Residues in contact with GLY 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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168A MET* 3.2 10.9 - - - -
169A PHE* 2.9 59.0 + - - -
171A LYS* 5.6 0.2 - - - +
189A PHE 3.2 8.3 - - - -
190A TYR* 4.0 9.3 - - - -
242A LEU 3.9 1.6 - - - -
243A TRP* 1.3 73.9 - - - +
245A LEU* 1.3 60.2 + - - -
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Residues in contact with LEU 245 (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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153A PHE* 4.8 2.0 - - + -
164A VAL* 4.1 28.5 - - + +
167A ALA* 3.7 19.5 - - + -
168A MET* 4.0 11.0 - - + -
169A PHE* 4.1 0.8 - - - -
188A ASN* 3.4 2.8 - - - +
189A PHE* 2.8 50.8 + - + +
224A LEU* 4.2 0.2 - - - +
244A GLY* 1.3 73.0 - - - +
246A ASP* 1.3 75.7 + - - +
249A THR* 3.5 32.3 - - + -
250A PHE* 4.0 31.4 - - + +
254A ILE* 4.6 7.9 - - + -
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Residues in contact with ASP 246 (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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131A ILE* 3.9 19.6 - - + +
133A HIS* 5.5 0.3 + - - -
167A ALA* 3.9 14.4 + - - +
169A PHE* 4.4 7.9 - - + -
187A ASP 3.7 0.4 - - - -
188A ASN* 3.5 16.7 + - - +
244A GLY 4.2 1.0 - - - -
245A LEU* 1.3 81.7 - - - +
247A ARG* 1.3 58.3 + - - +
248A VAL* 3.1 14.3 + - + +
249A THR* 2.6 49.4 + - - -
250A PHE* 3.2 21.0 + - - +
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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