Contacts of the strand formed by residues 170 - 177 (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 LEU 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE 3.8 0.5 - - - +
74A SER* 3.1 22.2 - - - -
75A PHE* 2.9 48.2 + - + +
129A PHE* 3.8 21.5 - - + -
162A TRP* 3.8 16.4 - - + +
168A GLN 3.6 1.3 + - - +
169A SER* 1.3 73.0 - - - +
171A ASN* 1.3 62.2 + - - +
172A VAL* 4.0 4.6 - - + +
187A ALA* 3.9 15.0 - - + -
188A THR* 3.6 30.7 - - - +
189A TYR* 3.8 32.3 - - + +
195A TYR* 4.7 1.6 - - + -
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Residues in contact with ASN 171 (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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72A GLN* 6.1 4.0 - - + +
73A PHE 3.7 4.5 - - - +
74A SER* 3.4 19.8 - - - -
169A SER* 4.9 8.5 + - - -
170A LEU* 1.3 73.9 - - - +
172A VAL* 1.3 60.6 + - - +
186A VAL 3.9 0.9 - - - +
187A ALA* 3.2 3.1 - - - -
188A THR* 2.8 51.6 + - - +
189A TYR 5.2 0.4 - - - -
190A SER* 5.1 10.7 - - - +
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Residues in contact with VAL 172 (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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71A SER 3.8 1.0 - - - +
72A GLN* 3.2 10.2 - - - +
73A PHE* 2.8 77.4 + - + +
75A PHE* 4.0 5.2 - - + -
129A PHE* 3.8 29.6 - - + -
170A LEU* 4.0 15.5 - - + +
171A ASN* 1.3 79.6 - - - +
173A LEU* 1.3 64.1 + - - +
174A VAL* 4.0 14.6 - - + -
185A VAL* 4.1 6.7 - - + -
186A VAL 3.4 8.5 - - - +
187A ALA* 4.2 1.8 - - + -
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Residues in contact with LEU 173 (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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70A GLN* 3.5 40.6 - - + +
71A SER 3.6 4.0 - - - +
72A GLN* 4.2 18.6 - - + +
172A VAL* 1.3 75.5 - - - +
174A VAL* 1.3 62.5 + - - +
175A THR* 3.8 15.3 - - - +
184A ASP 3.7 1.2 - - - +
185A VAL* 3.5 2.6 - - - -
186A VAL* 2.9 47.4 + - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 4.5 5.5 - - + -
70A GLN* 3.3 3.6 - - - +
71A SER* 2.8 42.4 + - - +
73A PHE* 4.0 16.2 - - + -
90A PHE* 4.5 15.9 - - + -
127A VAL* 4.2 26.5 - - + -
172A VAL* 4.0 17.3 - - + -
173A LEU* 1.3 75.1 - - - +
175A THR* 1.3 64.6 + - - +
183A LEU* 3.7 25.8 - - + -
184A ASP 3.3 5.8 - - - +
185A VAL* 4.3 7.2 - - + -
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Residues in contact with THR 175 (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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68A ASN* 5.0 8.3 - - - +
69A PHE* 3.4 13.0 - - - +
70A GLN* 4.3 11.0 + - + +
173A LEU* 3.8 22.7 + - - +
174A VAL* 1.3 77.6 + - - +
176A PHE* 1.3 73.1 + - - +
177A ASN* 4.2 4.5 - - + +
182A ASN 3.6 1.1 - - - +
183A LEU* 3.3 6.4 - - - +
184A ASP* 2.8 45.5 + - - +
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Residues in contact with PHE 176 (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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58A LEU* 5.6 0.7 - - + -
66A VAL* 4.0 12.1 - - + -
67A ALA 3.4 22.9 - - - -
68A ASN* 3.4 12.5 + - - -
69A PHE* 2.9 61.0 + + + +
175A THR* 1.3 77.5 - - - +
177A ASN* 1.3 56.8 + - - +
178A PRO* 3.8 16.6 - - + -
181A ARG* 3.6 28.9 - - + -
182A ASN 3.5 12.1 - - - -
183A LEU* 4.1 12.6 - - + -
201A VAL* 3.3 29.4 - - + -
203A VAL* 3.6 27.8 - - + -
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Residues in contact with ASN 177 (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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68A ASN* 4.0 10.6 - - - +
175A THR* 4.2 4.9 - - + -
176A PHE* 1.3 74.4 - - - +
178A PRO* 1.3 56.2 - - - +
179A SER* 2.8 29.7 + - - -
180A THR* 3.5 21.9 + - - +
181A ARG* 2.6 36.9 + - - -
182A ASN* 3.1 11.7 + - + +
184A ASP* 5.7 2.7 - - - +
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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