Contacts of the strand formed by residues 170 - 177 (chain B) in PDB entry 2ARB
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE 3.8 0.5 - - - +
74B SER* 3.1 22.9 - - - -
75B PHE* 2.9 46.9 + - + +
129B PHE* 3.7 21.5 - - + -
162B TRP* 3.7 19.5 - - + +
168B GLN 3.6 0.6 + - - +
169B SER* 1.3 73.3 - - - +
171B ASN* 1.3 61.4 + - - +
172B VAL* 3.9 4.6 - - + +
187B ALA* 3.9 14.1 - - + -
188B THR* 3.4 29.2 - - - +
189B TYR* 3.7 32.1 - - + +
195B TYR* 4.6 2.5 - - + -
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Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN* 3.1 24.5 + - - +
73B PHE 3.6 1.3 - - - -
74B SER* 3.6 22.6 - - - -
169B SER* 4.7 9.4 - - - +
170B LEU* 1.3 73.8 - - - +
172B VAL* 1.3 60.1 + - - +
186B VAL 3.9 0.7 - - - +
187B ALA* 3.2 3.5 - - - -
188B THR* 2.8 47.2 + - - +
230B SER* 5.1 0.8 + - - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER 3.8 0.6 - - - +
72B GLN* 3.2 9.6 + - - +
73B PHE* 2.8 68.8 + - + +
75B PHE* 4.0 5.6 - - + -
129B PHE* 3.7 29.8 - - + -
170B LEU* 3.9 20.2 - - + +
171B ASN* 1.3 80.5 - - - +
173B LEU* 1.3 63.3 + - - +
174B VAL* 3.9 14.4 - - + -
185B VAL* 4.1 8.7 - - + -
186B VAL 3.4 8.5 - - - +
187B ALA* 4.1 2.0 - - + -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLN* 4.3 15.9 - - + +
71B SER 3.5 15.5 - - - +
72B GLN* 4.0 22.2 - - + -
172B VAL* 1.3 74.3 - - - +
174B VAL* 1.3 61.5 + - - +
175B THR* 3.8 26.4 + - + +
184B ASP 3.7 1.2 - - - +
185B VAL* 3.5 2.9 - - - -
186B VAL* 2.8 47.0 + - + +
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 4.0 5.6 - - + +
70B GLN* 3.3 2.8 - - - -
71B SER* 2.8 42.6 + - - +
73B PHE* 3.9 24.9 - - + -
90B PHE* 4.3 15.9 - - + -
127B VAL* 4.2 27.1 - - + -
172B VAL* 3.9 10.3 - - + -
173B LEU* 1.3 74.0 - - - +
175B THR* 1.3 65.4 + - - +
183B LEU* 3.8 26.0 - - + -
184B ASP 3.4 6.7 - - - +
185B VAL* 4.3 5.8 - - + -
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Residues in contact with THR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 5.8 0.9 - - - -
69B PHE* 3.4 8.3 - - - -
70B GLN* 3.6 24.0 - - + -
173B LEU* 3.8 26.9 - - + -
174B VAL* 1.3 81.0 - - - +
176B PHE* 1.3 62.1 - - - +
177B ASN* 4.3 0.8 - - - +
182B ASN 3.7 0.6 - - - +
183B LEU* 3.3 8.0 - - - +
184B ASP* 2.8 51.6 + - - +
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 5.6 0.2 - - + -
66B VAL* 3.9 13.5 - - + -
67B ALA 3.4 24.7 - - - -
68B ASN* 3.5 13.5 + - - -
69B PHE* 3.0 58.4 + + + -
175B THR* 1.3 77.6 - - - +
177B ASN* 1.3 57.8 + - - +
178B PRO* 3.9 15.7 - - + -
181B ARG* 3.7 26.9 - - + -
182B ASN 3.4 13.2 - - - -
183B LEU* 4.2 12.6 - - + -
201B VAL* 3.4 26.7 - - + -
202B ASP* 5.2 0.2 - - - -
203B VAL* 3.5 31.0 - - + -
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 4.0 9.0 + - - +
175B THR* 4.3 0.6 - - - +
176B PHE* 1.3 74.5 - - - +
178B PRO* 1.3 56.8 - - - +
179B SER* 2.9 25.5 + - - -
180B THR* 3.6 25.0 + - - +
181B ARG* 2.7 35.0 + - - -
182B ASN* 3.1 11.1 + - + +
184B ASP* 6.0 1.6 - - - +
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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