Contacts of the strand formed by residues 65 - 78 (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 ARG 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 5.9 0.6 + - - -
12A PRO* 5.7 2.4 - - - +
2B ASP* 2.9 41.5 + - - -
59B TRP* 3.3 5.5 - - - +
60B GLU* 2.9 50.7 + - + +
63B SER* 3.1 26.7 + - - +
64B SER* 1.3 80.8 - - - +
66B VAL* 1.3 63.5 + - - +
204B ARG* 5.3 0.3 - - - -
237B LEU* 3.8 30.1 + - + +
238B LEU 3.3 25.8 - - - +
239B TYR* 3.9 41.0 + - + -
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Residues in contact with VAL 66 (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* 3.6 8.5 - - + +
59B TRP* 4.0 1.6 - - + -
64B SER 4.2 5.1 + - - +
65B ARG* 1.3 80.5 - - - +
67B ALA* 1.3 65.9 + - - +
176B PHE* 3.9 8.3 - - + -
178B PRO* 3.7 31.5 - - + +
203B VAL* 3.8 28.9 - - + -
204B ARG* 3.7 30.7 - - + +
237B LEU* 3.8 4.7 - - - -
238B LEU 3.1 22.3 + - - +
240B THR* 5.0 10.7 + - + +
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Residues in contact with ALA 67 (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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56B VAL* 5.7 0.7 - - + -
57B HIS 3.9 15.5 - - - +
58B LEU* 2.8 30.9 + - + +
66B VAL* 1.3 76.6 - - - +
68B ASN* 1.3 64.0 + - - +
69B PHE* 3.9 3.0 + - + +
176B PHE* 3.4 26.7 - - - -
178B PRO* 3.6 3.5 - - - +
235B SER* 4.7 7.9 - - - -
236B THR 3.3 19.3 - - - +
237B LEU* 3.6 4.8 - - + +
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Residues in contact with ASN 68 (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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67B ALA* 1.3 72.3 - - - +
69B PHE* 1.3 69.4 + - - +
70B GLN* 4.4 16.6 - - - +
175B THR* 5.8 0.6 - - - -
176B PHE 3.5 14.8 + - - +
177B ASN* 4.0 10.6 + - - +
178B PRO* 3.6 14.6 - - + +
234B THR* 4.0 0.3 - - - +
235B SER* 3.3 1.9 - - - -
236B THR* 2.9 35.2 + - + +
238B LEU* 3.1 26.1 - - + +
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Residues in contact with PHE 69 (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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56B VAL* 6.4 0.4 - - + -
58B LEU* 3.9 30.1 - - + -
67B ALA* 4.4 4.5 - - + -
68B ASN* 1.3 75.9 + - - +
70B GLN* 1.3 75.5 + - - +
71B SER* 4.9 1.1 - - - -
90B PHE* 4.6 5.4 - + - -
92B ILE* 3.5 29.8 - - + -
174B VAL* 4.6 12.3 - - + -
175B THR* 3.4 1.2 - - - -
176B PHE* 3.0 66.6 + + + +
183B LEU* 4.2 17.0 - - + -
203B VAL* 5.2 5.4 - - + -
233B PHE* 4.0 21.1 - + + -
234B THR* 3.1 12.6 - - - +
235B SER* 3.9 12.1 - - - -
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Residues in contact with GLN 70 (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* 4.4 13.9 - - - +
69B PHE* 1.3 80.8 - - - +
71B SER* 1.3 61.0 + - - +
72B GLN 4.2 0.4 - - - -
173B LEU* 4.3 14.5 - - + +
174B VAL 3.3 7.0 - - - +
175B THR* 3.6 23.3 - - + +
232B SER 4.0 0.2 - - - +
233B PHE* 3.4 6.6 - - - -
234B THR* 2.9 50.1 + - + +
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Residues in contact with SER 71 (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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69B PHE* 4.9 1.5 - - - -
70B GLN* 1.3 74.4 - - - +
72B GLN* 1.3 59.2 + - - +
73B PHE* 3.8 9.3 - - - -
90B PHE* 3.5 34.3 - - - -
172B VAL 3.8 1.2 - - - +
173B LEU* 3.5 3.0 - - - +
174B VAL* 2.8 40.9 + - - +
231B TRP* 3.0 26.9 + - - -
232B SER 3.4 4.3 - - - -
233B PHE* 3.9 7.4 - - - -
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Residues in contact with GLN 72 (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 4.2 0.6 - - - -
71B SER* 1.3 72.8 - - - +
73B PHE* 1.3 78.1 + - - +
171B ASN* 3.1 31.4 + - - +
172B VAL 3.2 15.1 + - - +
173B LEU* 4.0 18.6 - - + -
230B SER* 4.4 8.7 + - - -
231B TRP* 3.3 2.4 - - - +
232B SER* 2.8 50.8 + - - +
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Residues in contact with PHE 73 (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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71B SER* 3.8 12.3 - - - -
72B GLN* 1.3 89.2 - - - +
74B SER* 1.3 63.0 + - - +
75B PHE* 4.1 20.6 - + - -
88B ILE* 6.0 0.9 - - + -
89B ALA 6.2 0.2 - - - -
90B PHE* 3.8 28.0 - + + -
129B PHE* 4.1 13.9 - + - -
170B LEU 3.8 0.2 - - - +
171B ASN* 3.6 1.9 - - - -
172B VAL* 2.8 64.8 + - + +
174B VAL* 3.9 22.7 - - + -
215B PHE* 3.5 35.4 - + + -
228B LEU* 4.2 4.3 - - + -
230B SER 3.3 15.3 - - - +
231B TRP* 4.1 2.0 - - + -
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Residues in contact with SER 74 (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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73B PHE* 1.3 76.9 - - - +
75B PHE* 1.3 63.8 + - - +
169B SER* 4.9 3.1 - - - -
170B LEU 3.1 12.8 - - - -
171B ASN* 3.6 23.6 - - - -
228B LEU* 3.7 5.9 - - - +
229B GLU* 2.9 44.2 + - - +
230B SER* 2.8 25.4 + - - -
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Residues in contact with PHE 75 (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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73B PHE* 4.1 17.5 - + - -
74B SER* 1.3 75.8 - - - +
76B SER* 1.3 65.1 + - - +
77B LEU* 3.9 32.5 - - + -
88B ILE* 3.8 31.2 - - + -
129B PHE* 3.6 39.7 - + + -
162B TRP* 4.2 6.7 - + - -
168B GLN 3.9 0.2 - - - +
169B SER* 3.3 2.3 - - - -
170B LEU* 2.9 61.9 + - + +
172B VAL* 4.0 8.3 - - + -
227B THR 3.1 18.8 - - - +
228B LEU* 4.2 3.6 - - + -
229B GLU* 3.9 5.4 - - - -
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Residues in contact with SER 76 (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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75B PHE* 1.3 78.0 - - - +
77B LEU* 1.3 67.1 + - - +
78B LYS* 4.4 11.6 + - - -
167B GLY* 4.4 11.2 - - - -
168B GLN 3.7 23.3 - - - -
169B SER* 4.1 1.6 - - - -
225B THR* 4.7 0.3 + - - -
227B THR* 3.0 41.3 + - - +
229B GLU* 2.8 24.8 + - - -
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Residues in contact with LEU 77 (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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75B PHE* 3.9 21.8 - - + -
76B SER* 1.3 82.1 - - - +
78B LYS* 1.3 61.7 + - - +
87B GLY* 5.6 0.4 - - - -
88B ILE* 4.4 5.8 - - + -
129B PHE 5.4 1.1 - - - +
131B THR* 3.7 29.8 - - + -
162B TRP* 4.0 17.7 - - + -
164B ARG* 3.9 20.0 - - + +
165B ARG 4.1 3.7 + - - +
166B ASP* 3.6 6.1 - - - -
167B GLY 2.8 22.9 + - - +
168B GLN 4.7 2.0 + - - -
224B GLN* 4.0 8.1 - - - +
225B THR* 3.3 17.0 - - - +
226B HIS* 3.6 26.2 - - + -
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Residues in contact with LYS 78 (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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42B PRO* 4.1 5.6 - - + +
76B SER* 4.4 14.3 + - - +
77B LEU* 1.3 72.8 - - - +
79B SER* 1.3 63.9 + - - +
164B ARG* 3.7 1.6 - - - -
166B ASP* 3.4 11.4 - - - +
167B GLY* 3.5 29.9 - - - +
224B GLN* 3.3 0.9 - - - -
225B THR* 2.9 48.4 + - + +
227B THR* 4.8 7.5 + - - +
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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