Contacts of the strand formed by residues 179 - 186 (chain C) in PDB entry 5IY8
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 THR 179 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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951B GLN* 5.6 3.1 + - - -
38C PHE* 3.6 23.0 + - + +
39C ILE* 4.5 10.4 - - - +
177C ASN* 3.2 17.7 + - - +
178C PRO* 1.3 86.5 - - - +
180C ALA* 1.3 62.6 + - - +
181C GLY* 3.8 12.2 + - - -
182C VAL* 3.8 23.0 - - + +
233C VAL* 4.1 20.4 - - + -
234C GLU 3.5 4.3 - - - +
236C CYS* 4.0 8.0 - - - +
244C ILE* 4.4 4.9 - - + -
6J ARG* 4.8 1.0 + - - -
10J CYS 4.3 8.1 - - - +
11J GLY* 4.7 4.2 - - - -
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Residues in contact with ALA 180 (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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959B GLU* 4.2 5.4 - - - +
179C THR* 1.3 73.2 - - - +
181C GLY* 1.3 55.7 + - - +
234C GLU* 2.8 30.1 + - + +
235C SER 3.6 20.6 - - - +
236C CYS* 3.6 9.6 - - - +
10J CYS* 3.8 24.7 - - - +
11J GLY 4.7 0.2 - - - -
12J LYS* 3.8 35.3 + - + +
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Residues in contact with GLY 181 (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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951B GLN* 5.6 5.6 - - - -
959B GLU* 4.4 13.9 - - - -
179C THR* 3.3 5.7 - - - -
180C ALA* 1.3 79.6 - - - +
182C VAL* 1.3 68.9 + - - +
183C ALA 4.3 0.2 - - - -
232C ASN 4.7 0.7 - - - -
234C GLU* 3.2 33.0 + - - +
10J CYS* 5.1 6.1 - - - -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956B PHE* 4.9 4.5 - - - -
958B CYS 4.2 0.3 - - - +
959B GLU 3.4 17.2 + - - +
960B GLY* 4.2 5.7 - - - -
35C ARG* 4.8 14.1 + - + +
38C PHE* 4.5 29.4 - - + -
39C ILE* 4.5 15.7 - - + -
179C THR* 3.8 24.9 - - + +
181C GLY* 1.3 79.3 - - - +
183C ALA* 1.3 73.6 + - - +
184C PHE* 3.8 4.6 + - + +
231C TYR* 4.7 7.2 - - + -
232C ASN 3.9 2.9 - - - +
233C VAL* 4.5 13.2 - - + -
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Residues in contact with ALA 183 (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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958B CYS 3.3 21.5 - - - +
959B GLU* 4.1 5.3 + - - -
182C VAL* 1.3 83.2 - - - +
184C PHE* 1.3 60.6 + - - +
208C TYR* 6.1 0.4 - - - +
230C TYR 4.3 1.1 - - - +
231C TYR* 3.5 6.0 - - - -
232C ASN* 3.2 48.4 + - + +
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Residues in contact with PHE 184 (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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956B PHE* 3.6 33.8 - + + -
958B CYS* 4.0 9.4 + - - +
1029B TYR* 3.3 16.0 - + - -
1034B GLY* 4.3 9.2 - - - -
28C LEU* 3.7 26.2 - - + -
31C ALA* 3.5 28.3 - - + -
32C ASN* 4.5 2.5 - - - -
35C ARG* 4.4 14.8 - - + +
182C VAL* 3.8 3.7 + - + +
183C ALA* 1.3 76.9 - - - +
185C GLU* 1.3 67.5 + - - +
186C TYR* 3.9 20.9 - + - -
229C PHE* 3.7 17.7 - + + -
230C TYR 3.3 7.9 - - - -
231C TYR* 3.2 29.8 - + + -
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Residues in contact with GLU 185 (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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958B CYS* 5.2 10.7 - - - +
1029B TYR* 3.3 23.8 - - + +
1036B LYS* 6.1 0.2 - - - +
184C PHE* 1.3 78.6 - - - +
186C TYR* 1.3 64.4 + - - +
188C PRO* 4.4 12.6 - - + +
206C SER* 3.5 27.4 + - - -
208C TYR* 3.7 30.5 - - + -
229C PHE* 3.5 1.2 - - - +
230C TYR* 2.6 43.0 + - + +
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Residues in contact with TYR 186 (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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1029B TYR* 4.2 5.8 + + - -
1034B GLY 3.8 18.4 - - - -
1035B ARG* 3.6 6.3 - - - +
1036B LYS* 3.1 50.6 + - + -
28C LEU* 4.4 7.4 - - + -
184C PHE* 3.9 16.4 - + - -
185C GLU* 1.3 78.8 - - - +
187C ASP* 1.3 82.3 + - + +
188C PRO* 3.7 1.9 - - - +
192C LEU* 5.5 0.2 - - + -
194C HIS* 2.6 43.9 + + - -
226C PRO* 4.0 22.0 - - + -
227C GLU 5.0 2.0 - - - +
228C ARG 4.3 5.4 - - - +
229C PHE* 3.3 31.4 - + + -
230C TYR* 4.7 1.6 - - - -
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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