Contacts of the strand formed by residues 179 - 185 (chain C) in PDB entry 4AY1
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 LEU 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58C HIS* 4.2 27.6 - - + +
96C LYS* 4.4 24.5 - - + -
98C LEU* 4.4 17.7 - - + -
138C ASP* 2.9 20.6 + - + +
139C GLY* 3.1 4.6 - - - -
140C LEU 2.8 25.5 + - - -
166C PHE* 3.4 6.5 - - - -
176C GLU* 6.6 0.2 - - + -
177C ARG* 4.3 12.8 - - - +
178C LEU* 1.3 73.9 - - - +
180C LEU* 1.3 60.9 + - - +
181C THR* 4.2 1.8 - - + -
205C ASP* 3.4 24.5 - - + +
206C PHE* 5.1 5.6 - - + -
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Residues in contact with LEU 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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140C LEU* 3.5 18.2 - - + +
142C VAL* 4.5 4.3 - - + -
159C ILE* 3.6 36.3 - - + +
162C LEU* 3.9 22.7 - - + -
163C ALA* 3.7 17.5 - - - +
166C PHE* 4.0 22.9 - - + -
177C ARG* 5.4 1.8 - - - +
178C LEU 3.8 0.8 + - - +
179C LEU* 1.3 73.0 - - - +
181C THR* 1.3 69.2 + - - +
203C ASP 3.9 20.4 - - - +
204C LEU* 3.6 9.8 - - + -
205C ASP* 2.8 41.9 + - - +
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Residues in contact with THR 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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60C ILE* 4.7 0.3 - - - +
98C LEU* 3.7 17.1 - - + +
140C LEU 2.9 7.6 + - - +
141C ASP* 2.8 31.9 + - - +
142C VAL* 2.8 24.6 + - - +
179C LEU* 5.0 1.6 - - + -
180C LEU* 1.3 82.8 - - - +
182C ALA* 1.3 63.2 + - - +
204C LEU* 4.1 5.9 - - - +
205C ASP* 4.7 2.0 - - + -
206C PHE* 3.4 54.1 - - + +
208C ASN* 3.6 8.9 + - - -
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Residues in contact with ALA 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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141C ASP* 3.5 3.8 - - - -
142C VAL* 3.1 19.1 - - + +
155C PHE* 4.3 12.3 - - + -
159C ILE* 5.2 0.9 - - + -
181C THR* 1.3 79.0 - - - +
183C GLY* 1.3 60.7 + - - +
184C VAL* 3.6 15.7 + - + +
204C LEU* 3.7 24.4 - - + +
206C PHE 3.5 4.9 + - - -
207C ILE* 3.4 5.0 - - - -
208C ASN* 2.8 24.9 + - - +
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Residues in contact with GLY 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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32C TYR* 4.1 2.5 - - - -
141C ASP* 3.4 3.0 + - - -
142C VAL 3.4 2.7 + - - +
143C SER* 3.1 40.2 + - - -
144C TRP 4.1 8.3 + - - +
145C ILE* 4.7 0.3 - - - +
155C PHE* 5.7 1.2 - - - -
182C ALA* 1.3 70.7 - - - +
184C VAL* 1.3 63.0 + - - +
195C TYR* 4.5 0.7 + - - -
208C ASN* 3.2 16.4 - - - -
210C LEU* 3.7 15.5 - - - +
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Residues in contact with VAL 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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145C ILE* 5.8 0.2 - - - -
155C PHE* 5.1 3.1 - - + -
182C ALA* 3.6 22.9 - - + +
183C GLY* 1.3 80.0 - - - +
185C SER* 1.3 64.2 + - - +
195C TYR* 3.4 20.6 - - + +
200C LEU* 5.5 0.9 - - + -
204C LEU* 5.3 0.9 - - + -
207C ILE* 3.8 29.4 - - + -
208C ASN 3.1 7.7 + - - +
209C LEU* 3.9 2.9 - - - -
210C LEU* 2.9 33.0 + - - +
252C TRP* 3.3 40.2 - - + +
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Residues in contact with SER 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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146C TYR* 3.7 29.5 + - - -
184C VAL* 1.3 72.7 - - - +
186C ALA* 1.3 58.0 + - - +
187C GLY* 3.0 17.2 + - - -
190C MET* 3.4 26.5 - - - +
191C ILE* 3.3 7.8 - - - +
195C TYR* 3.0 20.1 + - - -
209C LEU* 3.6 0.4 - - - +
210C LEU* 4.3 5.0 - - - +
252C TRP* 3.0 25.8 + - - -
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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