Contacts of the strand formed by residues 181 - 185 (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 ASN 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D GLU* 3.4 6.1 - - - +
145D PHE* 3.0 55.0 + - + +
147D ALA 2.5 31.3 + - - +
149D ALA* 3.5 19.1 - - - +
169D LEU* 3.9 6.8 - - + +
171D ALA 3.6 6.9 - - - +
172D GLY* 3.4 10.0 - - - -
178D SER* 3.1 33.6 + - - -
179D GLU 4.1 0.2 - - - -
180D LYS* 1.3 77.4 - - - +
182D PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 182 (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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142B PHE* 3.6 35.7 - + - -
170B TYR* 5.2 3.4 - - - -
182B PHE* 3.9 23.1 - + - -
142D PHE* 3.5 26.2 - + + -
143D MET 3.4 2.5 - - - -
144D GLU* 3.7 27.8 - - + -
145D PHE* 4.1 3.1 - - - -
169D LEU* 3.7 4.7 - - - +
170D TYR* 3.1 43.3 + - + -
171D ALA* 2.8 31.3 + - + +
172D GLY 3.8 19.7 - - - -
180D LYS* 4.2 13.5 - - - -
181D ASN* 1.3 79.1 - - - +
183D GLY* 1.3 59.3 + - - +
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Residues in contact with GLY 183 (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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141D THR 3.8 0.2 - - - +
142D PHE* 3.8 4.3 - - - -
143D MET* 2.9 43.6 + - - -
145D PHE* 3.9 9.7 - - - -
168D ILE 3.2 12.3 - - - -
170D TYR* 3.6 12.5 - - - -
182D PHE* 1.3 74.9 - - - +
184D VAL* 1.3 62.3 + - - -
185D TYR 3.4 0.7 + - - -
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Residues in contact with VAL 184 (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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77D GLU* 4.4 12.8 - - + -
78D ASP 3.5 35.4 - - - +
79D LEU* 4.6 5.6 - - + -
141D THR* 3.7 10.1 - - - +
143D MET* 4.1 1.3 - - - -
167D GLY* 3.2 25.8 - - - -
168D ILE* 2.8 23.9 + - + +
170D TYR* 3.9 17.9 - - + -
183D GLY* 1.3 69.3 - - - -
185D TYR* 1.3 60.9 + - - +
186D PHE* 3.5 11.7 + - + -
190D LEU* 4.0 25.1 - - + -
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Residues in contact with TYR 185 (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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106D GLY* 3.7 9.8 - - - -
107D ALA* 3.1 39.5 + - + -
138D ILE* 4.2 22.7 - - + -
140D GLY 3.3 21.3 - - - -
141D THR* 2.9 26.4 + - - +
142D PHE 4.1 1.3 - - - -
143D MET* 4.0 25.1 - - + -
166D ILE* 3.7 32.1 - - + -
183D GLY 3.4 3.2 + - - -
184D VAL* 1.3 70.9 - - - +
186D PHE* 1.3 74.0 + - - +
187D THR* 3.2 14.9 + - + -
190D LEU* 3.4 13.9 - - - +
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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