Contacts of the strand formed by residues 177 - 182 (chain C) in PDB entry 3ARE
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 177 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 4.3 6.5 - - - -
141C PHE 3.2 9.2 - - - -
142C THR* 4.1 12.1 - - - -
144C PHE* 3.8 3.9 - - - -
163C LYS* 3.6 0.9 - - - -
164C CYS 3.1 31.4 + - - +
166C LEU* 3.8 14.5 - - - +
175C SER* 5.9 0.2 - - - -
176C ASN* 1.3 78.8 - - - +
178C ALA* 1.3 56.9 + - - +
145D THR* 6.1 0.7 - - - -
174D CYS* 4.3 0.2 - - - -
196D ARG* 2.7 48.8 + - - -
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Residues in contact with ALA 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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140C LEU* 3.7 4.1 - - - +
141C PHE* 2.8 36.1 + - + +
144C PHE* 4.2 0.8 - - + -
150C VAL* 3.8 30.5 - - + -
161C THR* 3.5 21.5 - - - +
162C ASP 4.1 3.8 - - - +
163C LYS 4.5 0.2 - - - +
177C SER* 1.3 74.8 - - - +
179C VAL* 1.3 63.8 + - - +
193C PHE* 3.6 11.9 - - + -
196D ARG* 3.7 2.7 - - - +
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Residues in contact with VAL 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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138C VAL* 4.1 13.7 - - + -
139C CYS 3.3 7.2 - - - +
140C LEU* 3.9 22.0 - - + -
159C TYR 4.0 0.3 - - - +
160C ILE* 3.4 2.6 - - - +
161C THR* 2.8 44.6 + - + +
178C ALA* 1.3 77.9 - - - +
180C ALA* 1.3 63.6 + - - +
181C TRP* 4.0 18.8 - - + -
193C PHE* 4.0 1.8 - - - -
147D VAL* 4.0 29.4 - - + -
149D LEU* 4.3 4.3 - - + -
194D SER* 4.1 8.1 - - - +
196D ARG* 3.9 19.5 - - - +
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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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138C VAL* 3.7 0.7 - - - -
139C CYS* 2.8 41.5 + - - +
158C VAL* 5.1 0.4 - - + -
159C TYR 3.2 4.3 - - - +
160C ILE* 3.6 24.0 - - + -
179C VAL* 1.3 75.5 - - - +
181C TRP* 1.3 63.9 + - - +
187C PHE* 4.4 5.2 - - + -
192C ALA* 4.2 14.4 - - + -
193C PHE* 3.6 23.5 - - + -
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Residues in contact with TRP 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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137C SER 4.0 9.9 - - - +
138C VAL* 3.8 16.8 - - + -
159C TYR* 3.0 75.7 + + + -
161C THR* 3.8 25.6 - - + -
179C VAL* 4.0 13.2 - - + -
180C ALA* 1.3 79.0 - - - +
182C SER* 1.3 66.1 + - - +
183C ASN 5.3 0.2 - - - -
187C PHE* 4.2 7.9 - - - -
149D LEU* 3.5 40.8 - - + +
151D THR* 4.1 8.6 - - + +
180D LEU* 4.2 8.1 - - + -
182D GLU* 5.9 0.2 - - + -
192D ALA* 3.7 32.8 - - + -
194D SER* 4.7 1.8 - - - -
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Residues in contact with SER 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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137C SER 5.3 2.0 + - - +
157C ASP* 3.1 19.6 + - - +
158C VAL* 3.8 10.9 - - - +
159C TYR* 5.1 0.2 - - - -
181C TRP* 1.3 81.8 - - - +
183C ASN* 1.3 66.2 + - - +
184C LYS* 3.3 22.2 + - - +
187C PHE* 3.5 40.7 - - - +
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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