Contacts of the strand formed by residues 175 - 182 (chain C) in PDB entry 5I4A
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 SER 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C LYS* 4.2 12.8 - - - -
166C TYR* 4.9 14.7 - - - -
167C LEU 3.1 13.7 + - - -
168C TYR* 3.9 15.6 - - - +
173C GLY 4.2 1.2 + - - -
174C LYS* 1.3 75.1 + - - +
176C PHE* 1.3 72.8 + - - +
177C PRO* 4.7 1.0 - - - +
207C ASN* 5.0 3.7 + - - +
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Residues in contact with PHE 176 (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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166C TYR* 3.4 5.6 - - - -
167C LEU* 2.8 36.7 + - + +
169C ASN* 4.4 6.1 - - + -
172C SER* 4.7 1.3 - - - -
174C LYS* 3.5 44.6 - - + -
175C SER* 1.3 86.6 - - - +
177C PRO* 1.3 70.4 - - + +
188C ILE* 3.8 27.6 - - + -
189C ASP 3.4 15.5 - - - +
190C ILE* 3.5 27.4 - - + -
204C TYR* 4.0 25.4 - + - -
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Residues in contact with PRO 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C GLY 3.3 9.9 - - - +
166C TYR* 3.9 26.0 - - + +
175C SER 4.7 0.9 - - - +
176C PHE* 1.3 88.2 - - + +
178C TYR* 1.3 62.9 + - - +
179C ILE* 3.5 4.2 + - + -
188C ILE* 3.6 5.5 - - - +
189C ASP* 3.2 55.0 + - + +
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Residues in contact with TYR 178 (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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157C ALA 6.0 0.4 - - - -
163C LYS* 3.5 27.8 - - + +
164C SER 3.2 22.9 - - - +
165C GLY* 2.7 21.8 + - - +
167C LEU* 3.7 35.0 - - + -
176C PHE 3.5 0.8 + - - -
177C PRO* 1.3 71.0 - - - +
179C ILE* 1.3 65.4 + - - +
180C SER* 3.4 23.5 - - - -
181C GLY* 2.9 26.2 + - - -
186C LEU* 3.7 13.7 - - + -
187C LYS 4.3 1.3 - - - -
206C PHE* 3.6 24.2 - + + -
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Residues in contact with ILE 179 (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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177C PRO* 3.5 3.1 + - + +
178C TYR* 1.3 80.2 - - - +
180C SER* 1.3 71.2 + - - +
187C LYS* 3.2 13.6 + - + +
188C ILE 3.4 7.6 - - - +
189C ASP* 3.3 44.6 - - + +
195C ILE* 3.4 44.0 - - + -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C TYR* 3.4 14.5 - - - -
179C ILE* 1.3 88.9 - - - +
181C GLY* 1.3 59.1 + - - +
182C LEU* 4.8 14.9 + - - +
185C ILE 3.7 2.1 + - - +
186C LEU* 3.6 0.7 - - - -
187C LYS* 2.7 61.2 + - - +
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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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158C LEU* 3.7 21.7 - - - +
163C LYS* 4.8 7.6 - - - -
178C TYR* 2.9 24.1 + - - -
180C SER* 1.3 72.9 - - - +
182C LEU* 1.3 71.1 + - - +
185C ILE 3.3 8.5 - - - -
186C LEU* 4.4 0.2 - - - -
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Residues in contact with LEU 182 (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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158C LEU* 4.5 0.2 - - - +
180C SER* 4.2 13.5 + - - +
181C GLY* 1.3 83.8 - - - +
183C ASP* 1.3 84.5 + - - +
184C GLY 3.2 2.7 - - - -
185C ILE* 3.1 23.4 + - - +
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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