Contacts of the strand formed by residues 194 - 200 (chain A) in PDB entry 2ARE
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A VAL* 3.6 31.0 - - + +
187A ALA 3.3 3.6 - - - +
188A THR* 3.7 20.7 - - + +
192A GLY 3.1 9.1 + - - +
193A THR* 1.3 78.7 - - - +
195A TYR* 1.3 74.1 + - - +
196A GLU* 2.6 34.6 + - + +
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.9 18.3 - - + +
160A VAL* 4.6 8.7 - - + -
161A LYS 3.5 19.5 - - - -
162A TRP* 3.6 35.7 - + - -
163A ASP* 2.6 38.6 + - - +
165A ARG* 4.7 1.2 + - - -
170A LEU* 4.7 0.4 - - + -
185A VAL* 3.8 1.1 - - - +
186A VAL* 3.4 0.5 - - - -
187A ALA* 2.8 47.3 + - + +
189A TYR* 3.6 25.7 - + - -
193A THR* 3.5 25.8 - - + +
194A ARG* 1.3 78.4 - - - +
196A GLU* 1.3 68.6 + - - +
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.9 18.9 - - - +
185A VAL* 3.2 8.5 - - - +
186A VAL* 4.3 12.0 - - + +
194A ARG* 2.6 43.2 + - + +
195A TYR* 1.3 80.7 - - - +
197A VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 4.0 24.2 - - + +
148A GLY 5.3 0.2 - - - -
149A ILE* 4.1 14.1 - - + -
158A LYS* 3.6 38.4 - - + +
159A THR 4.3 9.6 - - - +
160A VAL* 3.9 11.2 - - + -
184A ASP 3.7 0.2 - - - -
185A VAL* 2.8 54.6 + - + +
196A GLU* 1.3 76.1 - - - +
198A SER* 1.3 65.4 + - - +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 3.8 4.0 - - - -
158A LYS* 3.8 18.5 - - - +
182A ASN* 5.5 3.8 + - - -
183A LEU 3.2 5.8 - - - -
184A ASP* 2.9 30.5 - - - -
197A VAL* 1.3 77.6 - - - +
199A TYR* 1.3 65.9 + - - +
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Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 3.8 20.2 - - + -
151A VAL* 4.3 13.5 - - + -
157A VAL* 3.6 46.0 - - + +
158A LYS* 4.4 13.5 - - + -
182A ASN* 3.6 4.9 - - - -
183A LEU* 2.8 34.7 + - + +
198A SER* 1.3 79.4 - - - +
200A GLU* 1.3 89.0 + - - +
201A VAL* 3.7 17.2 + - + -
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A THR 3.9 17.0 - - - +
181A ARG* 3.3 24.3 - - + +
182A ASN* 3.8 10.9 + - - +
199A TYR* 1.3 95.5 - - - +
201A VAL* 1.3 61.4 + - - +
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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