Contacts of the strand formed by residues 138 - 146 (chain C) in PDB entry 2WNU
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 TYR 138 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C SER* 3.3 38.8 + - - -
130C PHE* 3.6 23.7 - + - -
132C CYS* 4.1 12.1 - - - -
133C LYS 4.8 0.9 + - - -
134C VAL* 2.6 37.6 + - - +
136C GLY 3.3 23.8 - - - -
137C LEU* 1.3 75.8 - - - +
139C TYR* 1.3 59.7 + - - +
140C PHE* 3.6 25.2 - + + -
179C VAL 3.9 0.3 - - - +
180C LEU* 3.2 9.2 - - - +
181C LEU 2.8 34.7 + - - +
183C LEU* 4.0 12.6 - - + -
211C GLY 5.1 0.4 - - - -
212C PHE* 3.4 9.9 - - - -
213C LEU* 3.5 28.6 - - + +
214C LEU* 5.0 0.4 - - - -
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Residues in contact with TYR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 4.8 5.4 - + - -
142B TYR* 4.3 10.1 + + - -
144B THR* 3.7 35.5 + - + +
146B HIS* 4.6 4.7 + - - -
216B SER* 5.2 0.9 - - - -
218B PHE* 4.0 13.9 - + - -
137C LEU 4.4 0.2 + - - -
138C TYR* 1.3 73.3 - - - +
140C PHE* 1.3 77.0 + - - +
141C VAL* 3.8 36.5 - - + +
178C GLY* 4.7 1.5 - - - -
179C VAL 3.5 14.1 - - - -
180C LEU* 3.5 28.0 - - + -
210C SER 4.5 0.2 - - - -
211C GLY* 3.0 5.4 - - - -
212C PHE* 3.0 71.7 + + + -
214C LEU* 4.1 6.6 - - + +
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Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C PHE* 4.0 22.2 - + - -
130C PHE* 3.9 22.7 - + - -
138C TYR* 3.6 26.5 - + + -
139C TYR* 1.3 78.4 - - - +
141C VAL* 1.3 63.5 + - - +
154C LEU* 3.9 19.7 - - + -
178C GLY* 3.0 4.4 - - - -
179C VAL* 2.9 38.1 + - + +
181C LEU* 4.2 20.9 - - + -
183C LEU* 3.9 12.3 - - + -
189C VAL* 3.9 32.8 - - + -
209C PHE* 3.8 18.4 - + + -
210C SER 3.4 1.8 - - - +
211C GLY* 4.0 13.2 - - - -
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 3.2 31.2 - - + +
146B HIS* 4.7 7.0 - - + +
139C TYR* 3.8 31.6 - - + +
140C PHE* 1.3 75.0 - - - +
142C TYR* 1.3 63.6 + - - +
143C HIS* 3.8 24.2 - - + +
177C GLY 3.4 14.6 - - - +
178C GLY* 4.1 0.2 - - - -
208C VAL* 5.6 0.2 - - - +
209C PHE* 3.4 4.2 - - - -
210C SER* 2.7 53.6 + - - +
212C PHE* 5.1 1.8 - - + -
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Residues in contact with TYR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 5.3 0.7 - + + -
141C VAL* 1.3 75.2 - - - +
143C HIS* 1.3 76.4 + - - +
144C ALA* 3.9 11.7 - - + -
152C VAL* 3.3 38.1 - - + +
154C LEU* 5.5 6.1 - - + -
164C PHE* 3.5 23.5 - + - +
175C ASN* 2.8 39.7 + - - -
176C SER* 3.4 2.8 - - - -
177C GLY* 3.1 50.4 + - - +
178C GLY* 4.4 0.7 - - - -
191C LEU* 3.6 37.7 - - + -
208C VAL* 3.2 15.3 - - - +
209C PHE* 3.9 2.7 - + + -
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Residues in contact with HIS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A TYR* 4.1 8.8 + - - -
140A THR* 4.3 6.0 + - - -
142A GLN* 4.9 2.2 - - - -
167A PHE* 3.9 9.4 - - + -
180A SER* 3.0 37.9 + - - +
181A GLY* 3.7 27.3 + - - -
182A GLY 3.8 3.6 - - - -
146B HIS* 5.3 2.2 - + - -
182B THR* 4.8 4.3 - - + -
141C VAL* 3.8 21.7 - - + +
142C TYR* 1.3 80.3 + - - +
144C ALA* 1.3 60.3 + - - +
174C VAL* 3.8 11.2 - - + -
175C ASN 3.5 3.8 - - - -
176C SER* 3.8 9.3 - - - -
206C ASP 3.8 3.3 - - - +
207C SER* 3.2 4.0 - - - -
208C VAL* 2.8 48.7 + - + +
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Residues in contact with ALA 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C PHE* 6.0 1.3 - - + -
142C TYR* 3.9 15.0 - - + -
143C HIS* 1.3 73.5 - - - +
145C SER* 1.3 62.9 + - - +
146C HIS* 3.6 1.9 + - - -
150C LEU* 3.9 16.6 - - + -
152C VAL* 4.5 3.1 - - + -
174C VAL* 3.4 3.0 - - - +
175C ASN* 2.7 46.0 + - - +
199C MET* 3.8 26.0 - - + -
207C SER* 3.4 4.3 - - - -
208C VAL 5.7 0.2 - - - +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PHE* 4.5 0.5 - - - -
144C ALA* 1.3 71.4 - - - +
146C HIS* 1.3 62.1 + - - +
172C ASN* 4.0 1.8 - - - -
173C GLN 3.3 6.1 - - - -
174C VAL* 3.8 10.6 - - - +
199C MET* 3.3 28.6 - - - +
201C GLY* 3.8 8.5 + - - -
205C SER* 2.5 42.7 + - - -
206C ASP 2.8 23.9 + - - -
207C SER* 3.1 8.9 + - - -
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ALA 3.6 8.7 + - - -
145C SER* 1.3 74.4 - - - +
147C THR* 1.3 64.0 + - - +
148C ALA 2.6 22.4 - - - +
150C LEU* 3.7 15.8 - - + +
166C GLY* 3.2 27.6 + - - -
167C HIS 4.3 0.4 + - - -
168C THR* 3.4 22.3 - - + +
172C ASN* 3.5 3.2 + - - -
173C GLN* 3.0 51.5 + - + +
174C VAL 4.2 1.6 - - - -
175C ASN* 3.7 28.5 - - + -
198C ASP* 3.2 31.0 - - - +
200C VAL 3.8 2.7 - - - -
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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