Contacts of the strand formed by residues 64 - 77 (chain A) in PDB entry 2BUK
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 GLN 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ARG* 4.8 0.2 - - - +
61A SER 3.7 5.7 + - - +
62A GLY 3.5 0.8 + - - -
63A ASP* 1.3 83.7 - - + +
65A VAL* 1.3 72.4 + - - +
153A LEU* 4.0 25.2 - - + +
154A VAL 3.3 5.2 - - - +
155A ASN* 2.8 30.8 + - - +
194A ASP* 3.3 15.1 - - - +
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Residues in contact with VAL 65 (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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51A ILE* 4.7 5.6 - - + -
60A ARG* 3.8 37.7 - - + -
64A GLN* 1.3 83.6 - - - +
66A ARG* 1.3 64.7 + - - +
67A ILE* 4.6 7.4 - - + -
153A LEU* 3.5 4.7 - - - +
154A VAL* 2.9 56.0 + - + -
156A TYR* 3.9 12.6 - - + +
192A TYR* 4.0 18.2 - - + -
193A THR 3.7 11.9 - - - +
194A ASP* 4.1 3.1 - - - +
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Residues in contact with ARG 66 (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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65A VAL* 1.3 77.0 - - - +
67A ILE* 1.3 64.6 + - - +
68A VAL* 3.3 3.4 + - + +
152A GLN* 3.8 9.3 - - - +
153A LEU* 4.0 39.9 - - + +
192A TYR* 2.8 5.7 - - - -
193A THR* 2.8 53.1 + - - +
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Residues in contact with ILE 67 (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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48A SER* 4.9 6.3 - - - -
51A ILE* 5.5 2.9 - - + -
65A VAL* 4.6 5.2 - - + -
66A ARG* 1.3 70.4 - - - +
68A VAL* 1.3 60.4 + - - +
69A SER 3.7 26.2 - - - +
70A HIS* 3.9 19.5 - - + +
151A GLY* 2.9 38.5 - - - +
152A GLN* 3.0 14.6 + - - +
154A VAL* 3.8 28.5 - - + -
171A ILE* 4.3 8.3 - - + -
188A TYR* 3.7 21.1 - - - +
190A ALA* 4.3 11.0 - - + -
191A VAL 3.4 5.8 - - - +
192A TYR* 3.7 10.5 - - + -
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Residues in contact with VAL 68 (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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21A ASN* 4.9 3.1 - - - +
26A HIS* 3.9 33.4 - - + +
66A ARG* 4.0 5.4 - - + +
67A ILE* 1.3 73.7 - - - +
69A SER* 1.3 65.7 + - - +
150A PRO* 3.5 8.3 - - - +
151A GLY 3.2 11.8 + - - -
191A VAL* 2.5 22.3 + - + +
192A TYR* 4.3 2.0 - - - -
193A THR* 3.9 19.7 - - + +
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Residues in contact with SER 69 (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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67A ILE* 3.4 4.5 - - - +
68A VAL* 1.3 86.9 - - - +
70A HIS* 1.3 62.0 + - - +
148A ASN* 4.6 15.4 + - - -
149A LEU 3.3 15.0 - - - -
150A PRO* 4.6 0.9 - - - -
151A GLY 4.0 1.8 - - - +
189A GLU* 5.5 1.4 + - - +
190A ALA* 3.6 0.3 - - - -
191A VAL* 2.9 42.5 + - - +
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Residues in contact with HIS 70 (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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67A ILE* 3.9 18.0 - - + +
69A SER* 1.3 76.0 - - - +
71A LYS* 1.3 59.3 + - - +
89A TRP* 3.6 24.4 - + - -
128A LEU* 3.9 14.4 - - + +
148A ASN* 3.5 4.1 - - - +
149A LEU* 2.9 50.9 + - - +
150A PRO 4.0 11.9 + - - -
151A GLY* 4.4 4.4 - - - -
171A ILE* 3.8 30.6 - - + +
188A TYR* 2.8 31.6 + - + +
189A GLU* 3.0 16.8 - - - +
190A ALA* 4.1 1.3 - - - -
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Residues in contact with LYS 71 (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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28A ARG* 5.8 0.6 - - - +
70A HIS* 1.3 74.0 - - - +
72A LEU* 1.3 64.0 + - - +
73A HIS* 6.0 0.7 - - + -
89A TRP* 4.3 0.7 - - - -
146A ILE* 3.6 28.9 - - + -
147A ILE 3.1 14.6 - - - +
148A ASN* 3.6 19.8 + - + +
187A SER 4.5 0.4 - - - -
188A TYR* 3.2 10.9 - - - -
189A GLU* 2.8 61.4 + - + +
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Residues in contact with LEU 72 (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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47A LEU* 4.2 22.0 - - + -
71A LYS* 1.3 76.0 - - - +
73A HIS* 1.3 66.0 - - - +
74A VAL* 4.2 13.0 - - + -
87A PHE* 5.6 2.2 - - + -
89A TRP* 3.6 55.4 - - + -
145A ARG 3.6 2.0 - - - +
146A ILE* 3.3 3.5 - - - +
147A ILE* 2.8 43.8 + - + +
173A MET* 4.1 28.7 - - + -
186A SER* 4.8 3.1 - - - -
187A SER 3.5 16.6 - - - +
188A TYR* 4.4 5.2 - - + -
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Residues in contact with HIS 73 (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 LYS* 6.0 0.9 - - + -
72A LEU* 1.3 74.6 - - - +
74A VAL* 1.3 69.3 + - - +
75A ARG* 5.4 4.2 - - + +
144A ASP* 2.7 32.4 + - + +
145A ARG 3.3 14.6 - - - -
146A ILE* 3.7 29.5 - - + +
185A ASP 3.7 0.2 - - - +
186A SER* 2.9 29.5 - - - -
187A SER* 2.9 31.0 + - - +
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Residues in contact with VAL 74 (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 LEU* 4.2 14.1 - - + -
73A HIS* 1.3 78.9 - - - +
75A ARG* 1.3 61.0 + - - +
87A PHE* 3.5 55.4 - - + -
131A VAL* 4.7 4.3 - - + -
133A LEU* 4.3 4.0 - - + +
144A ASP* 3.0 5.2 - - - +
145A ARG* 2.8 54.0 + - + +
147A ILE* 4.8 5.8 - - + -
173A MET* 4.0 15.3 - - - -
185A ASP 3.5 3.4 - - - -
186A SER* 4.8 2.0 - - - -
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Residues in contact with ARG 75 (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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73A HIS* 5.4 4.5 - - + -
74A VAL* 1.3 74.6 - - - +
76A GLY* 1.3 59.6 + - - +
77A THR* 3.8 15.7 + - - -
87A PHE* 4.0 4.4 - - - -
133A LEU* 4.9 0.2 - - - -
142A ILE* 3.3 35.7 - - + +
143A LYS 3.3 15.7 - - - +
144A ASP* 3.5 17.3 - - + -
183A LEU 4.6 0.2 - - - -
184A TRP* 2.9 9.9 - - - +
185A ASP* 2.8 66.1 + - + +
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Residues in contact with GLY 76 (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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75A ARG* 1.3 75.8 - - - +
77A THR* 1.3 64.2 + - - -
85A PHE* 3.9 21.8 - - - -
87A PHE* 5.0 0.9 - - - -
133A LEU* 4.5 3.3 - - - +
135A CYS* 3.0 21.7 - - - -
142A ILE* 3.4 3.5 - - - +
143A LYS 2.9 24.7 + - - +
183A LEU 3.4 5.6 - - - -
184A TRP* 4.3 0.4 - - - -
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Residues in contact with THR 77 (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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75A ARG* 3.8 21.1 + - - -
76A GLY* 1.3 75.9 + - - -
78A ALA* 1.3 75.2 + - - +
79A ILE* 3.9 12.1 - - + +
85A PHE* 3.5 4.7 - - - -
141A SER* 3.3 8.3 - - - +
142A ILE* 3.8 20.5 - - + +
182A GLY* 3.4 4.5 - - - -
183A LEU* 2.7 41.7 + - + -
185A ASP* 5.0 0.9 + - - -
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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