Contacts of the strand formed by residues 135 - 141 (chain D) in PDB entry 2WJZ
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 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D GLU* 4.2 8.7 - - - +
126D VAL 2.8 31.0 + - - -
127D ILE* 5.0 0.2 - - - +
133D PRO 3.5 1.4 + - - -
134D ASN* 1.3 75.3 - - - +
136D TYR* 1.3 68.0 + - - -
137D TYR* 3.3 11.3 - - - -
185D ILE* 3.6 9.4 - - - -
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 3.5 21.1 + - - -
3C ALA* 3.9 18.4 - - + -
242C LYS* 5.3 4.3 + - - -
247C ASN* 3.0 29.2 + - - -
248C VAL 4.4 12.5 + - - -
249C ARG* 3.8 33.0 + - + -
250C LEU 4.8 8.7 - - - -
123D TRP* 3.4 25.1 - - + -
124D ASN 3.5 17.7 - - - -
125D GLU* 3.7 32.7 + - + +
135D GLY* 1.3 75.9 - - - -
137D TYR* 1.3 61.4 + - - +
185D ILE* 3.5 21.9 - - - +
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D TRP* 3.2 6.7 - - - -
124D ASN 3.0 30.4 + - - -
126D VAL* 3.6 21.1 - - + -
128D PHE* 3.8 8.5 - + - -
133D PRO* 2.6 46.5 + - - +
135D GLY 3.3 21.1 - - - -
136D TYR* 1.3 73.5 - - - +
138D ALA* 1.3 59.2 + - - +
139D PHE* 3.2 9.1 - - + -
177D PHE* 3.4 44.9 - + + -
179D PRO* 5.0 0.4 - - + -
182D SER* 3.5 18.4 - - - +
185D ILE* 3.6 31.3 - - + +
186D GLY* 4.3 1.8 - - - -
189D LEU* 3.9 11.8 - - + +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PRO* 4.5 11.0 - - + -
122D GLY 3.7 7.0 - - - +
123D TRP* 3.9 16.0 - - + +
137D TYR* 1.3 70.2 - - - +
139D PHE* 1.3 61.8 + - - +
140D VAL* 5.3 1.8 - - + -
177D PHE* 3.3 0.7 - - - +
178D HIS* 2.8 36.9 + - + +
181D ALA* 3.4 33.4 - - + +
182D SER* 3.0 11.2 + - - +
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D HIS* 3.4 26.5 - + + +
121D MET* 3.4 0.5 - - - -
122D GLY 2.8 33.8 + - - +
124D ASN* 3.3 40.4 - - + -
126D VAL* 3.4 26.9 - - + -
137D TYR 3.2 21.3 - - - -
138D ALA* 1.3 74.1 - - - +
140D VAL* 1.3 74.2 + - - +
141D HIS* 3.8 20.6 - + + -
156D THR* 3.6 9.6 - - + -
163D PHE* 4.5 3.8 - + - -
165D SER* 3.7 16.6 - - - -
176D GLN* 4.3 7.0 - - + -
177D PHE* 3.6 28.0 - + + +
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Residues in contact with VAL 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN* 3.7 39.8 + - + +
51D VAL* 5.3 6.9 - - - +
84D CYS* 5.9 1.0 - - - +
119D PRO* 4.8 3.1 - - + -
120D HIS 3.2 6.3 - - - +
121D MET* 4.4 16.6 - - + -
122D GLY 5.0 0.2 - - - +
138D ALA* 4.3 2.4 + - + -
139D PHE* 1.3 86.3 - - - +
141D HIS* 1.3 64.0 + - - +
176D GLN 5.2 2.6 + - - +
178D HIS* 4.4 27.2 + - + +
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Residues in contact with HIS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D GLN* 4.9 2.7 - - - +
113D LEU* 3.8 15.9 - - + +
119D PRO* 4.0 5.2 - - - +
120D HIS* 2.9 62.4 + - - +
139D PHE* 3.8 17.2 - + + -
140D VAL* 1.3 79.0 - - - +
142D THR* 1.3 62.0 + - - +
143D TYR 2.8 26.6 + - - +
144D ARG* 4.8 0.4 - - + -
163D PHE* 3.5 32.8 - + - -
176D GLN* 3.6 30.6 - - + +
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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