Contacts of the strand formed by residues 167 - 173 (chain A) in PDB entry 1JVN
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 LYS 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ASN* 4.0 32.3 + - + +
133A LEU 5.5 1.7 + - - +
134A PHE* 3.4 23.8 - - + -
162A GLU* 5.9 0.2 - - - -
165A GLY 4.6 5.8 - - - +
166A TRP* 1.3 76.0 - - - +
168A ILE* 1.3 61.6 + - - +
182A VAL* 3.5 2.8 - - - -
183A ASN* 2.7 51.1 + - + +
184A LYS* 5.8 0.4 - - - -
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Residues in contact with ILE 168 (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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105A ILE* 5.1 0.4 - - + -
130A SER* 4.6 11.1 + - - -
132A ASN* 4.9 5.6 + - - +
133A LEU* 4.8 0.9 - - - +
134A PHE* 4.0 4.8 - - - -
153A LEU* 4.5 4.7 - - + -
158A LYS* 5.7 4.9 - - + +
161A LEU* 3.9 33.2 - - + -
166A TRP* 3.8 20.1 + - + +
167A LYS* 1.3 80.0 - - - +
169A ALA* 1.3 72.7 + - - +
170A LYS* 3.8 21.0 + - + +
179A ILE* 3.8 24.0 - - + -
181A ALA 3.7 3.1 - - - +
182A VAL* 3.5 29.4 - - + -
806A SO4 5.5 1.6 + - - -
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Residues in contact with ALA 169 (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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127A CYS* 4.3 8.7 - - - -
133A LEU* 4.0 17.3 - - + -
134A PHE* 3.8 5.7 - - + -
137A LEU* 3.6 30.7 - - + -
168A ILE* 1.3 73.2 - - - +
170A LYS* 1.3 60.8 + - - +
179A ILE* 3.8 1.7 - - - -
180A ALA* 2.7 27.4 + - - +
181A ALA* 2.8 24.2 + - + +
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Residues in contact with LYS 170 (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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127A CYS* 3.2 8.2 - - - +
128A ILE* 2.7 63.7 + - + +
129A PRO 5.3 0.8 + - - -
130A SER* 4.7 11.7 - - - -
153A LEU* 4.0 19.3 - - + -
158A LYS* 4.0 19.5 - - + +
168A ILE* 3.8 15.4 + - + +
169A ALA* 1.3 74.8 - - - +
171A ALA* 1.3 59.5 + - - +
177A GLU* 3.6 28.9 - - + +
178A PHE 3.5 9.2 - - - +
180A ALA* 4.1 0.7 - - - -
806A SO4 4.2 16.6 + - - -
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Residues in contact with ALA 171 (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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125A ASN* 4.7 4.0 - - - -
126A SER 3.4 20.0 - - - +
128A ILE* 4.1 6.7 - - - -
145A PHE* 4.5 4.7 - - + -
170A LYS* 1.3 74.7 - - - +
172A LYS* 1.3 60.4 + - - +
177A GLU* 3.4 5.0 - - - +
178A PHE* 2.8 59.8 + - + +
180A ALA* 3.8 16.4 - - + -
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Residues in contact with LYS 172 (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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125A ASN* 2.9 20.5 + - - +
128A ILE* 4.2 11.9 - - + -
171A ALA* 1.3 77.2 - - - +
173A TYR* 1.3 62.1 + - - +
174A GLY 3.4 22.7 - - - +
175A SER* 4.4 11.4 - - - +
176A GLU 3.2 16.4 - - - +
177A GLU* 4.6 9.6 - - + +
178A PHE* 4.0 0.4 - - - -
231A TYR* 3.4 56.4 + - + +
234A TYR 3.8 1.6 - - - +
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Residues in contact with TYR 173 (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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112A PHE* 4.0 18.8 - + + -
117A LYS* 3.2 39.4 - - + -
118A PRO* 2.4 43.3 + - - +
120A PRO 4.2 0.9 + - - -
121A GLU* 3.3 53.2 - - + +
125A ASN* 4.5 0.2 - - - -
172A LYS* 1.3 73.0 - - - +
174A GLY* 1.3 64.6 + - - +
176A GLU* 2.9 22.5 + - - +
178A PHE* 3.9 11.4 - - + -
234A TYR* 3.4 28.8 - + + -
236A LEU* 3.6 28.0 - - + +
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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