Contacts of the strand formed by residues 55 - 66 (chain C) in PDB entry 3HB8
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 THR 55 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C VAL 3.4 0.7 - - - +
46C ARG* 3.2 4.2 - - - +
47C LYS* 2.8 39.6 + - - +
49C ASP* 4.7 5.4 - - + +
54C GLY* 1.3 83.1 - - - +
56C LEU* 1.3 60.9 + - - +
57C SER* 3.6 4.2 + - - -
256C HIS* 3.8 20.6 - - + +
257C ILE 3.0 18.2 - - - -
258C TYR* 3.5 42.4 - - + -
259C LEU* 3.7 10.2 - - - +
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 3.0 35.7 - - + +
41C LEU* 4.0 22.0 - - + +
44C GLY* 4.8 1.8 - - - -
45C VAL* 3.6 8.1 - - - +
46C ARG* 4.0 24.0 - - + +
55C THR* 1.3 75.0 - - - +
57C SER* 1.3 58.6 + - - +
256C HIS* 3.1 1.4 - - - -
257C ILE* 2.7 33.9 + - + +
259C LEU* 4.7 10.5 - - + -
262C ILE* 3.9 28.5 - - + -
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLY 3.9 0.3 - - - -
45C VAL* 2.9 39.3 + - - +
47C LYS* 4.3 21.4 - - - +
55C THR* 3.6 3.1 + - - -
56C LEU* 1.3 73.2 - - - +
58C VAL* 1.3 71.6 + - - +
59C PHE* 4.7 0.9 + - - +
254C ASP* 2.7 36.7 + - - -
255C ALA 3.5 3.1 - - - -
256C HIS* 3.8 5.4 - - - -
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 4.1 22.4 - - + +
40C ILE* 3.7 38.6 - - + -
43C CYS 4.5 2.9 - - - +
44C GLY* 3.7 12.3 - - - +
57C SER* 1.3 85.5 + - - +
59C PHE* 1.3 66.6 + - - +
60C GLY 3.8 3.0 + - - +
61C MET* 4.2 19.0 - - + +
253C GLY 3.2 1.2 - - - +
254C ASP 3.9 0.2 - - - -
255C ALA* 2.9 33.1 + - - +
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C SER* 5.6 0.9 - - - +
58C VAL* 1.3 77.3 - - - +
60C GLY* 1.3 63.3 + - - +
213C TYR* 4.8 9.2 - - - -
215C ARG 5.3 0.4 - - - -
253C GLY* 3.2 32.5 - - - -
254C ASP* 3.7 10.8 - - + +
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Residues in contact with GLY 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 3.8 4.3 + - - +
59C PHE* 1.3 77.8 - - - +
61C MET* 1.3 67.1 + - - +
252C LEU 3.4 8.2 + - - -
253C GLY* 2.9 15.2 + - - -
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Residues in contact with MET 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN* 3.5 42.8 - - + +
39C HIS* 4.9 8.5 - - - -
40C ILE* 3.5 33.7 - - + -
58C VAL* 4.2 16.6 - - + -
60C GLY* 1.3 80.2 - - - +
62C GLN* 1.3 64.6 + - - +
219C MET* 4.1 5.6 - - - -
251C THR* 3.6 4.7 - - - +
252C LEU* 2.8 38.8 + - + +
255C ALA* 3.4 31.0 - - + -
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C GLN* 3.8 6.7 + - - +
61C MET* 1.3 79.9 - - - +
63C ALA* 1.3 66.8 + - - +
64C ARG* 5.3 5.4 + - - -
211C GLN* 3.3 13.7 - - - +
249C ILE* 3.6 20.2 - - + +
250C HIS 3.3 6.3 - - - +
251C THR* 3.0 26.9 + - + +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN* 4.0 16.6 - - + -
36C GLN* 3.9 18.2 - - + +
62C GLN* 1.3 80.4 - - - +
64C ARG* 1.3 60.9 + - - +
65C TYR* 3.7 28.6 - - + +
248C PHE 3.8 0.9 - - - +
249C ILE* 3.5 4.0 - - - +
250C HIS* 2.8 37.2 + - + +
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Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 5.1 0.3 - - - -
32C GLN* 3.2 30.1 + - - +
62C GLN* 5.3 5.7 + - - -
63C ALA* 1.3 75.5 - - - +
65C TYR* 1.3 70.3 + - - +
66C SER 4.3 0.8 + - - +
247C ASP* 3.5 41.4 + - + -
248C PHE 3.7 2.0 - - - -
249C ILE* 3.9 29.2 - - + +
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Residues in contact with TYR 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 3.4 36.6 - - - -
30C GLU* 4.8 1.8 - - - -
32C GLN* 4.3 2.7 - - + -
33C TYR* 3.2 32.9 + - + +
36C GLN* 4.0 4.0 + - - -
63C ALA* 3.7 30.7 - - + +
64C ARG* 1.3 77.5 - - - +
66C SER* 1.3 64.7 + - - +
67C LEU* 3.5 2.1 + - - +
72C PRO* 3.8 27.8 - - + -
74C LEU* 5.0 3.8 - - + -
227C ILE* 3.6 29.9 - - + +
247C ASP* 3.2 4.0 - - - -
248C PHE* 2.8 58.9 + + + +
250C HIS* 4.1 9.7 + - + -
276C PHE* 5.0 3.4 - + + -
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Residues in contact with SER 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLY* 5.9 2.8 - - - -
64C ARG 4.3 0.6 + - - -
65C TYR* 1.3 73.4 - - - +
67C LEU* 1.3 57.8 + - - +
68C ARG* 3.1 42.4 + - - +
70C GLU* 3.3 36.4 + - - +
72C PRO* 3.6 12.1 - - - +
246C GLY 4.0 3.1 - - - -
247C ASP* 4.1 1.8 - - - -
276C PHE* 6.4 0.2 - - - -
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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