Contacts of the strand formed by residues 179 - 185 (chain D) in PDB entry 4U8T
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 ARG 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D HIS 4.3 6.1 - - - +
178D SER* 1.3 78.2 - - - +
180D PHE* 1.3 68.2 + - - +
181D PHE* 4.2 16.5 - - + -
213D ALA* 3.3 34.8 + - - +
216D SER* 4.9 9.1 - - - -
217D LEU* 4.3 14.6 - - + +
222D LYS 3.2 5.1 + - - +
223D ILE* 3.3 10.8 - - + +
224D TYR* 3.1 22.9 + - - -
300D GLU* 2.9 42.6 + - - +
301D ILE 5.5 0.2 - - - -
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Residues in contact with PHE 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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174D VAL* 3.7 23.1 - - + -
178D SER* 3.8 16.8 - - - -
179D ARG* 1.3 79.1 - - - +
181D PHE* 1.3 62.9 + - - +
224D TYR* 3.5 41.1 - + + +
226D LEU* 5.1 7.2 - - + -
300D GLU* 3.3 10.0 + - - +
301D ILE* 2.9 36.9 + - + +
303D ALA* 3.7 31.0 - - + -
306D SER* 3.1 36.8 - - - +
307D LYS* 4.7 6.1 - - + -
310D LEU* 4.1 18.8 - - + -
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Residues in contact with PHE 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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179D ARG* 4.2 17.5 - - + -
180D PHE* 1.3 76.9 - - - +
182D VAL* 1.3 67.1 + - - +
183D ILE* 5.2 0.2 - - + -
209D ARG* 4.3 19.3 - - + -
210D LEU* 3.7 23.1 - - + -
213D ALA* 3.9 29.6 - - + -
223D ILE* 3.8 25.6 - - + -
224D TYR 2.9 10.0 + - - +
225D LEU* 3.5 7.6 - - + +
226D LEU* 2.9 27.4 + - - +
298D THR* 3.5 24.2 - - - -
299D GLN 3.3 3.8 - - - -
300D GLU* 3.6 35.2 - - + -
301D ILE* 4.3 4.5 - - - -
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Residues in contact with VAL 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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181D PHE* 1.3 71.4 - - - +
183D ILE* 1.3 70.8 + - - +
184D LYS* 4.2 11.7 - - + -
226D LEU* 3.7 4.9 - - + -
235D PHE* 4.1 24.7 - - + -
292D VAL* 4.1 7.9 - - + -
295D SER* 3.8 31.0 - - - +
296D ARG 4.0 13.0 - - - +
298D THR* 2.8 29.1 + - - -
299D GLN* 2.9 15.6 + - + +
301D ILE* 3.6 24.4 - - + +
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Residues in contact with ILE 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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181D PHE* 3.7 0.4 + - + -
182D VAL* 1.3 81.3 - - - +
184D LYS* 1.3 68.4 + - - +
200D TRP* 3.5 37.5 - - + +
202D SER* 5.3 0.4 - - - -
210D LEU* 4.0 27.8 - - + -
225D LEU* 3.8 32.8 - - + -
226D LEU 2.9 12.8 + - - +
227D PHE* 3.6 28.3 - - + -
228D SER* 2.9 27.2 + - - -
297D ASP* 3.7 11.0 - - - +
298D THR* 4.3 3.6 - - + -
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Residues in contact with LYS 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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182D VAL* 4.2 8.3 - - + -
183D ILE* 1.3 81.0 - - - +
185D SER* 1.3 59.6 + - - +
228D SER* 2.7 39.6 + - - +
229D VAL 3.6 9.3 + - - -
230D ASN* 3.6 15.3 - - - +
235D PHE* 5.6 2.6 - - - -
293D THR 5.1 3.2 + - - -
295D SER 3.8 18.2 - - - +
297D ASP* 3.2 20.6 + - + +
0T 6MZ 3.3 31.8 + - - +
1T C 3.3 35.4 + - - +
2T A 2.7 26.5 + - - -
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Residues in contact with SER 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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183D ILE* 5.6 0.4 - - - -
184D LYS* 1.3 74.4 - - - +
186D SER* 1.3 60.4 + - - +
187D SER* 2.7 34.1 + - - -
190D HIS* 4.0 0.9 - - - +
191D VAL* 3.7 20.2 - - - +
200D TRP* 3.8 13.5 - - - -
227D PHE* 5.6 0.9 - - - -
228D SER 3.1 9.2 + - - -
229D VAL* 3.4 3.5 - - - -
230D ASN 2.8 27.7 + - - -
0T 6MZ 3.4 22.0 + - - -
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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