Contacts of the strand formed by residues 175 - 182 (chain D) in PDB entry 5U03
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 PHE 175 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D TYR* 3.3 25.4 - - + -
5D LEU* 3.8 30.5 - - + -
145D ILE* 6.1 0.2 - - + -
163D PHE* 4.1 26.9 - + + -
166D PHE* 4.1 11.4 - + - -
167D GLN* 3.5 48.9 - - + +
170D VAL* 3.9 11.9 - - + -
171D LYS 4.1 3.6 - - - +
172D ARG* 2.9 16.3 + - - +
173D GLU 3.3 1.8 + - - -
174D ASN* 1.3 80.4 - - - +
176D CYS* 1.3 75.1 + - - +
177D ASN* 4.3 13.2 - - + -
209D LEU* 5.9 2.5 - - + -
212D ASP* 5.3 0.9 - - - -
269D ARG* 3.1 16.9 + - - -
270D LEU* 4.3 2.6 - - - +
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Residues in contact with CYS 176 (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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3D TYR 2.8 7.4 + - - +
4D ILE* 4.0 20.0 - - + -
5D LEU 2.8 27.0 + - - -
175D PHE* 1.3 83.1 - - - +
177D ASN* 1.3 63.1 + - - +
178D ILE* 3.6 27.1 + - - -
212D ASP* 3.4 20.4 - - - -
213D LEU* 5.3 0.9 - - - -
265D TYR* 5.3 0.2 - - - -
266D PHE* 3.6 20.4 - - + -
269D ARG* 4.8 5.8 - - + -
270D LEU* 4.1 11.7 - - + -
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Residues in contact with ASN 177 (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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5D LEU* 4.0 5.5 - - - +
7D THR* 3.8 12.1 + - - +
167D GLN* 5.4 3.2 + - - +
175D PHE* 4.3 14.3 - - + -
176D CYS* 1.3 73.0 - - - +
178D ILE* 1.3 74.0 + - - +
179D HIS* 3.9 1.6 + - - +
204D LEU* 4.3 4.5 - - - +
209D LEU* 3.4 36.6 - - - +
210D SER 3.4 24.5 - - - +
211D PRO* 3.5 14.2 - - - +
212D ASP* 2.7 39.9 + - - +
213D LEU 3.3 5.5 + - - -
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Residues in contact with ILE 178 (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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4D ILE* 3.5 27.4 - - + -
5D LEU 2.8 13.4 + - - +
6D VAL* 4.2 12.8 - - + -
7D THR* 2.8 31.4 + - - -
19D ILE* 5.2 6.7 - - + -
23D VAL* 6.6 0.2 - - + -
176D CYS* 3.6 23.6 - - - -
177D ASN* 1.3 77.4 - - - +
179D HIS* 1.3 62.6 + - - +
180D VAL* 4.5 8.3 - - + -
213D LEU* 3.7 21.8 - - + +
215D VAL* 3.9 26.5 - - + -
266D PHE* 4.0 16.2 - - + -
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Residues in contact with HIS 179 (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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7D THR* 3.0 20.3 + - - +
8D GLY* 3.6 25.9 - - - -
151D VAL* 3.7 13.7 - - + -
177D ASN* 3.9 0.6 + - - +
178D ILE* 1.3 75.6 - - - +
180D VAL* 1.3 64.0 + - - +
181D SER* 4.4 7.0 - - - -
200D SER* 2.9 33.6 + - - -
201D VAL* 3.8 24.3 - - + +
204D LEU* 3.6 14.6 - - + +
211D PRO* 3.5 24.0 - - + -
213D LEU 3.1 8.3 + - - +
214D VAL* 3.2 8.6 - - + +
215D VAL 2.7 30.0 + - - +
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Residues in contact with VAL 180 (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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6D VAL* 4.2 11.9 - - + -
7D THR 2.8 18.9 + - - +
8D GLY* 3.0 21.3 - - - -
9D GLY 3.0 7.6 + - - +
14D ILE* 3.6 35.3 - - + +
15D GLY 5.0 1.8 - - - -
16D LYS* 4.0 22.7 - - + +
19D ILE* 4.8 7.2 - - + -
178D ILE* 4.5 2.9 - - + -
179D HIS* 1.3 79.0 + - - +
181D SER* 1.4 66.2 + - - +
215D VAL* 3.4 32.8 - - + +
217D ARG* 5.1 2.0 - - + +
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Residues in contact with SER 181 (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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9D GLY 4.7 5.2 - - - +
10D VAL* 3.9 8.8 - - - +
14D ILE* 3.4 9.2 - - - +
179D HIS* 4.4 12.1 - - - -
180D VAL* 1.4 76.2 - - - +
182D LEU* 1.3 66.9 + - - -
197D THR* 2.7 44.3 + - - -
200D SER* 4.5 2.3 - - - -
214D VAL* 4.6 2.9 - - - -
215D VAL 2.8 12.3 + - - -
216D CYS* 4.5 2.2 - - - -
217D ARG* 2.9 28.4 + - - +
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Residues in contact with LEU 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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184C PRO* 5.9 8.1 - - + -
10D VAL* 3.8 31.4 - - + +
11D ILE* 4.5 10.5 - - + -
14D ILE* 3.6 22.2 - - + -
181D SER* 1.3 84.9 + - - +
183D VAL* 1.4 73.6 + - - +
184D PRO* 3.2 33.0 - - + +
193D LYS 4.2 1.2 - - - +
196D PRO* 4.4 1.4 - - - +
197D THR* 2.9 20.3 + - - -
217D ARG* 3.6 20.0 - - + +
218D CYS 6.2 0.2 - - - -
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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