Contacts of the strand formed by residues 165 - 171 (chain D) in PDB entry 2W7U
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 165 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.4 22.0 - - + -
29D VAL* 4.7 12.6 - - + -
35D VAL* 5.5 3.4 - - + -
101D THR* 3.9 11.9 - - + +
102D LYS 2.8 18.3 + - - +
103D PHE* 3.8 24.2 - - + -
104D ALA* 2.9 23.1 + - - +
157D PRO* 3.8 25.1 - - + -
158D VAL 4.1 1.6 - - - +
159D LEU* 3.8 10.2 - - + +
164D GLU* 1.3 68.9 - - - +
166D ILE* 1.3 60.8 + - - +
167D GLY 3.5 21.1 - - - +
168D ILE* 5.0 0.4 - - + -
186D PHE* 3.7 28.2 - - + +
191D LYS* 5.5 1.0 + - - -
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Residues in contact with ILE 166 (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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104D ALA* 4.0 8.5 - - + -
106D GLY 5.2 0.7 - - - -
107D ALA* 3.8 22.0 - - + +
111D ASP* 6.1 1.1 - - + +
113D ILE* 3.7 24.9 - - + -
135D ILE* 4.6 1.3 - - + -
143D MET* 4.2 12.6 - - - -
158D VAL* 2.9 14.6 + - + +
159D LEU 3.9 2.0 - - - -
160D ASN* 3.5 42.4 - - + +
164D GLU 4.0 1.3 - - - +
165D LEU* 1.3 76.0 - - - +
167D GLY* 1.3 58.8 + - - +
185D TYR* 3.7 30.2 - - + -
186D PHE* 3.1 31.8 + - - +
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Residues in contact with GLY 167 (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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143D MET* 3.9 9.4 - - - +
158D VAL 2.8 25.3 + - - -
165D LEU* 3.5 6.9 - - - +
166D ILE* 1.3 81.1 - - - +
168D ILE* 1.3 66.4 + - - +
184D VAL 3.2 14.6 - - - -
186D PHE* 3.7 14.8 - - - -
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Residues in contact with ILE 168 (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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27D VAL* 3.9 20.4 - - + -
35D VAL* 4.1 12.1 - - + +
36D THR 3.7 20.6 - - - +
37D ASN* 3.5 22.9 - - - +
78D ASP 3.6 14.8 - - - +
79D LEU* 4.2 12.6 - - + -
143D MET* 4.2 0.2 - - - +
155D GLY* 3.7 13.7 - - - +
156D SER 3.2 11.4 - - - +
158D VAL* 4.3 3.1 - - - -
165D LEU* 5.0 0.2 - - + -
167D GLY* 1.3 79.7 - - - +
169D LEU* 1.3 64.9 + - - +
183D GLY* 3.2 3.7 - - - -
184D VAL* 2.8 42.0 + - + +
186D PHE* 4.0 13.9 - - + -
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Residues in contact with LEU 169 (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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37D ASN* 3.0 9.5 - - - +
115D VAL* 4.5 11.4 - - + -
145D PHE* 3.7 30.3 - - + -
149D ALA* 4.1 18.2 - - + -
153D ASN* 3.4 33.2 - - + +
154D SER* 4.1 3.6 - - - -
155D GLY* 2.9 21.0 + - - -
156D SER* 2.9 14.9 + - - +
158D VAL* 4.1 4.1 - - + +
168D ILE* 1.3 73.4 - - - +
170D TYR* 1.3 74.3 + - - +
171D ALA 3.8 20.4 - - - +
172D GLY* 5.6 0.2 - - - -
181D ASN* 3.9 12.6 - - + +
182D PHE 3.7 11.9 - - - +
183D GLY* 4.2 1.8 - - - -
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Residues in contact with TYR 170 (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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182B PHE* 5.2 3.3 - - - -
37D ASN* 3.4 22.2 + - - +
39D HIS* 4.1 9.0 - - - -
78D ASP* 3.6 28.0 - - + +
142D PHE* 3.6 25.3 - + - -
154D SER* 3.7 11.5 + - - -
169D LEU* 1.3 78.0 - - - +
171D ALA* 1.3 73.8 + - + +
182D PHE* 3.1 30.4 + + + +
183D GLY 3.6 37.0 - - - -
184D VAL* 3.6 12.6 - - + -
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Residues in contact with ALA 171 (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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170B TYR* 6.1 0.7 - - - +
169D LEU* 3.8 10.0 - - - +
170D TYR* 1.3 104.7 - - + +
172D GLY* 1.3 63.0 + - - +
181D ASN* 3.6 5.5 - - - +
182D PHE* 2.8 43.0 + - + +
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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