Contacts of the strand formed by residues 153 - 157 (chain A) in PDB entry 2WJP
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 LEU 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.7 0.9 - - - +
105A PRO* 3.6 32.3 - - + +
107A VAL* 4.1 19.3 - - + -
122A VAL* 5.1 0.7 - - + -
126A ALA* 3.9 25.6 - - + -
131A VAL* 4.0 13.0 - - + -
132A ASN 3.4 2.2 + - - -
133A VAL* 3.3 6.0 - - + +
134A GLY 3.0 23.0 + - - -
151A CYS* 3.0 7.5 - - - -
152A GLU* 1.3 80.5 - - - +
154A TYR* 1.3 71.1 + - - +
155A VAL* 4.1 13.7 - - + -
282A ALA* 4.5 12.6 - - + +
284A LEU* 4.3 20.9 - - + -
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Residues in contact with TYR 154 (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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98A PHE* 3.6 33.4 - + + -
102A ALA* 3.9 18.2 - - + -
103A GLN 4.4 3.3 + - - -
104A ALA* 3.8 36.3 - - + -
105A PRO 2.9 9.7 + - - +
106A ILE* 3.4 12.8 - - + -
107A VAL* 2.9 25.1 + - - +
134A GLY* 3.3 12.3 - - - +
146A LEU* 3.6 24.5 - - + -
147A LEU* 3.5 7.8 - - + +
148A ASP 3.1 33.6 + - - -
151A CYS* 3.5 20.9 - - + -
153A LEU* 1.3 74.7 - - - +
155A VAL* 1.3 64.8 + - - +
156A LEU* 4.1 6.1 - - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.5 7.9 - - + +
109A ILE* 3.8 18.4 - - + -
119A THR* 3.6 33.8 - - + +
122A VAL* 3.9 26.7 - - + -
123A GLY* 4.3 5.4 - - - +
133A VAL* 3.8 21.5 - - + -
134A GLY 2.9 9.5 + - - +
135A VAL* 3.4 8.5 - - + -
136A GLY 3.1 24.1 + - - +
153A LEU* 4.1 9.9 - - + -
154A TYR* 1.3 78.0 - - - +
156A LEU* 1.3 64.0 + - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 4.6 7.9 - - + -
98A PHE* 3.8 32.3 - - + -
99A CYS* 5.4 1.1 - - - -
106A ILE* 4.0 21.1 - - + -
107A VAL 2.9 11.8 + - - +
108A ALA* 3.6 1.7 - - - -
109A ILE* 2.9 28.3 + - - +
119A THR* 4.2 3.6 - - - -
136A GLY 3.4 9.6 - - - +
137A GLY* 4.5 0.7 - - - -
143A ALA* 4.3 14.4 - - + -
146A LEU* 3.9 25.4 - - + -
154A TYR* 4.6 6.5 - - + -
155A VAL* 1.3 80.3 - - - +
157A GLU* 1.3 60.7 + - - +
158A LEU* 3.7 28.6 + - + +
169A LEU* 5.6 0.7 - - + -
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Residues in contact with GLU 157 (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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109A ILE 3.5 4.3 - - - -
115A LYS* 3.2 37.9 - - + +
116A SER* 2.6 37.3 + - - -
119A THR* 3.4 17.2 + - - +
136A GLY 3.0 11.1 + - - +
137A GLY* 3.8 0.9 - - - -
138A ASN* 2.9 51.1 + - + +
139A ILE* 3.1 27.8 - - + +
156A LEU* 1.3 72.2 - - - +
158A LEU* 1.3 68.3 + - - +
319A LYS* 5.3 4.0 + - - -
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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