Contacts of the strand formed by residues 258 - 270 (chain O) in PDB entry 3A0B
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 GLU 258 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78O VAL* 3.1 6.6 - - - +
79O LYS* 2.8 79.1 + - + +
81O GLU* 4.4 12.3 + - - +
91O PHE* 4.6 5.2 - - + -
244O GLU* 5.7 0.7 - - - +
246O LEU* 4.3 20.6 - - + +
257O HIS* 1.3 72.0 - - - +
259O VAL* 1.3 64.2 + - - +
260O LYS 4.3 0.2 - - - -
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Residues in contact with VAL 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O PHE* 4.6 4.5 - - + -
77O LEU 3.0 14.4 - - - +
78O VAL* 4.1 16.6 - - + -
91O PHE* 4.8 0.9 - - - -
142O ILE* 5.0 2.7 - - + -
144O LEU* 3.5 26.2 - - + -
243O SER 3.3 10.4 - - - +
244O GLU* 3.3 9.5 - - - +
245O GLN* 3.1 24.5 + - + +
247O SER* 4.4 15.0 - - - +
257O HIS 4.2 9.0 - - - +
258O GLU* 1.3 80.7 - - - +
260O LYS* 1.3 63.0 + - - +
261O ILE* 3.4 26.3 - - + +
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Residues in contact with LYS 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O PHE 3.5 0.5 - - - -
77O LEU* 2.6 52.4 + - + +
91O PHE* 3.3 46.3 - - + -
242O GLU* 3.5 29.2 + - - +
243O SER 3.3 9.0 - - - +
244O GLU* 3.9 21.4 + - + -
259O VAL* 1.3 70.6 - - - +
261O ILE* 1.3 74.4 + - - +
262O GLN* 4.7 8.3 - - - +
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Residues in contact with ILE 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O PRO* 4.2 5.2 - - + -
75O THR 3.6 11.4 - - - +
76O PHE* 3.6 28.5 - - + -
144O LEU* 3.4 32.8 - - + -
146O PHE* 3.3 40.4 - - + -
241O PHE* 3.8 1.8 - - - -
242O GLU* 2.9 6.0 - - - -
243O SER* 2.8 45.6 + - - +
245O GLN* 4.8 4.9 - - + +
259O VAL* 3.4 12.1 - - + +
260O LYS* 1.3 85.9 - - - +
262O GLN* 1.3 64.1 + - - +
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Residues in contact with GLN 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O PRO* 3.6 2.1 - - - +
74O THR* 2.7 31.0 + - - +
75O THR* 3.1 36.6 + - - +
77O LEU* 4.8 9.9 - - + +
240O THR* 6.4 0.2 - - - -
241O PHE* 3.0 26.0 - - - +
242O GLU* 3.8 21.8 - - + +
260O LYS* 4.7 7.7 - - + +
261O ILE* 1.3 75.6 - - - +
263O GLY* 1.3 51.4 + - - +
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Residues in contact with GLY 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O GLN 3.0 15.3 - - - -
73O PRO* 3.5 0.7 - - - -
74O THR* 3.1 18.4 - - - -
240O THR* 3.1 8.4 - - - -
241O PHE* 2.7 35.7 + - - -
262O GLN* 1.3 77.0 - - - +
264O VAL* 1.3 61.3 + - - -
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Residues in contact with VAL 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O CYS* 6.2 0.2 - - + -
46O PRO 5.8 2.2 - - - +
72O GLN* 2.5 58.4 + - - +
73O PRO 4.8 0.4 - - - +
74O THR* 4.2 8.0 + - - +
238O ALA* 5.1 4.0 - - + -
239O GLY 2.6 27.8 - - - +
240O THR* 4.0 6.7 - - + +
241O PHE* 3.0 4.4 - - - -
263O GLY* 1.3 75.6 - - - -
265O PHE* 1.3 70.6 + - - +
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Residues in contact with PHE 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O CYS* 4.3 6.8 - - - +
46O PRO 4.4 1.7 - - - +
69O LEU* 4.3 3.4 - - + -
70O CYS 3.0 16.8 - - - +
71O LEU* 4.2 4.7 - - + -
72O GLN 4.3 0.7 - - - +
168O PHE* 5.6 1.1 - + - -
225O LEU* 3.3 39.0 - - + -
226O ASN 3.9 11.4 - - - -
227O VAL* 4.4 12.8 - - + -
237O ILE* 3.2 33.4 - - + -
238O ALA* 3.6 8.0 - - - +
239O GLY* 2.8 56.0 + - - -
240O THR 3.8 9.2 - - - -
241O PHE* 3.9 13.0 - - + -
264O VAL* 1.3 80.5 - - - +
266O TYR* 1.3 87.0 + - - +
267O ALA* 4.2 5.4 - - + -
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Residues in contact with TYR 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O CYS* 4.1 7.6 - - + -
46O PRO* 2.9 57.0 - - + +
48O LEU* 5.9 1.8 - - + -
68O ARG* 3.5 29.0 - - + +
69O LEU* 3.2 1.6 - - - +
70O CYS* 2.4 41.5 + - + +
236O GLU* 3.8 32.6 + - + +
237O ILE 3.7 13.9 - - - -
238O ALA* 4.6 4.0 - - + -
265O PHE* 1.3 91.1 - - - +
267O ALA* 1.3 94.4 + - - +
268O SER* 3.4 19.3 + - - -
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Residues in contact with ALA 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O ILE* 3.5 26.9 - - + -
68O ARG 2.7 18.8 - - - +
69O LEU* 3.7 10.8 - - + -
237O ILE* 2.8 46.2 + - + +
265O PHE* 4.5 2.5 - - + -
266O TYR* 1.3 83.1 - - - +
268O SER* 1.3 58.9 + - - +
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Residues in contact with SER 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66O ILE* 4.1 2.4 - - - +
67O ALA* 3.1 34.0 + - - +
68O ARG* 3.3 11.5 + - - +
234O THR* 5.1 4.7 - - - -
235O GLY 3.3 8.7 - - - -
236O GLU* 4.1 10.8 - - - -
266O TYR* 3.4 25.3 + - - -
267O ALA* 1.3 73.3 - - - +
269O ILE* 1.3 71.4 + - - +
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Residues in contact with ILE 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O TYR* 3.7 39.5 - - + -
64O TYR* 4.0 11.9 - - + -
65O ARG 3.2 10.5 - - - +
66O ILE* 3.4 17.5 - - + -
67O ALA* 5.1 0.3 - - - +
111O LEU* 3.9 22.4 - - + -
162O ILE* 5.0 8.1 - - + -
234O THR* 4.4 10.6 - - - +
235O GLY* 3.1 20.0 + - - +
237O ILE* 3.6 34.1 - - + -
267O ALA 5.0 0.2 - - - -
268O SER* 1.3 85.1 + - - +
270O GLU* 1.3 70.6 + - - +
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Residues in contact with GLU 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O TYR* 5.0 0.6 + - - -
64O TYR* 3.2 6.1 - - - -
65O ARG* 2.6 56.9 + - - +
67O ALA* 3.7 26.9 + - + +
268O SER 4.3 2.5 - - - +
269O ILE* 1.3 84.5 - - - +
271O PRO* 1.3 78.3 - - + +
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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