Contacts of the strand formed by residues 55 - 66 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ARG* 3.2 4.2 - - - +
47D LYS* 2.6 47.1 + - + +
49D ASP* 5.2 2.9 - - + +
54D GLY* 1.3 81.7 - - - +
56D LEU* 1.3 66.0 + - - +
57D SER* 3.6 0.6 + - - -
256D HIS* 3.4 18.1 - - + +
257D ILE 2.4 41.0 + - - -
258D TYR* 3.3 27.4 - - + +
259D LEU* 3.8 14.9 - - - +
175E ARG* 4.9 6.7 - - - +
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ILE* 3.6 31.9 - - + +
41D LEU* 3.8 32.5 - - + +
44D GLY 3.7 20.6 - - - +
45D VAL 3.4 9.0 - - - -
46D ARG* 4.2 6.3 - - + +
55D THR* 1.3 75.1 + - - +
57D SER* 1.3 58.4 + - - +
256D HIS* 3.1 22.7 - - - -
257D ILE* 3.1 14.5 + - + +
259D LEU* 3.9 18.7 - - + +
262D ILE* 4.6 10.8 - - + -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D GLY* 3.4 1.9 - - - -
45D VAL* 2.5 43.9 + - - +
47D LYS* 3.6 22.4 - - - -
55D THR 4.5 0.4 - - - -
56D LEU* 1.3 75.0 - - - +
58D VAL* 1.3 64.9 + - - +
254D ASP* 2.9 28.6 + - - -
255D ALA 3.2 3.4 - - - -
256D HIS* 4.1 5.2 - - - -
202E TYR* 2.6 27.2 + - - -
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D HIS* 4.2 24.0 - - + +
40D ILE* 3.8 30.1 - - + +
43D CYS 4.3 4.0 - - - +
44D GLY* 3.4 29.6 - - - +
57D SER* 1.3 74.8 + - - +
59D PHE* 1.3 65.0 + - - +
61D MET* 4.3 16.6 - - + -
253D GLY 3.7 0.2 - - - +
254D ASP* 3.7 0.5 - - - -
255D ALA* 2.7 45.4 + - - +
64E ARG* 4.4 9.9 - - - +
202E TYR* 4.5 0.9 - - - -
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 1.3 75.3 - - - +
60D GLY* 1.3 60.0 + - - +
253D GLY* 3.1 33.4 - - - -
254D ASP 3.6 1.1 - - - -
64E ARG* 3.2 24.9 + - - -
200E GLN* 3.7 41.3 - - + -
202E TYR* 3.4 62.4 - + + -
209E SER* 3.9 7.2 - - - +
210E CYS 3.9 8.5 - - - -
211E GLN* 3.6 36.3 - - + -
249E ILE* 3.6 10.6 - - + +
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 4.0 1.6 + - - +
59D PHE* 1.3 72.2 - - - +
61D MET* 1.3 66.7 + - - +
252D LEU 3.3 7.2 - - - -
253D GLY 2.8 13.7 + - - -
62E GLN* 3.5 10.4 - - - +
64E ARG* 3.1 19.8 + - - -
211E GLN* 4.0 8.1 - - - -
249E ILE* 3.9 18.5 - - - +
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Residues in contact with MET 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLN* 3.4 57.0 - - + +
39D HIS* 3.4 29.8 - - + -
40D ILE* 4.0 12.1 - - + -
58D VAL* 4.3 10.5 - - + -
60D GLY* 1.3 79.3 - - - +
62D GLN* 1.3 65.1 + - - +
219D MET* 4.8 1.3 - - - -
251D THR* 3.4 0.7 - - - -
252D LEU* 2.8 41.6 + - + -
255D ALA* 3.5 28.3 - - + -
62E GLN* 3.1 13.0 + - - +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D GLN* 4.9 0.7 - - - +
36D GLN* 3.4 10.0 + - - +
61D MET* 1.3 80.3 - - - +
63D ALA* 1.3 65.3 + - - +
64D ARG* 5.4 0.6 + - - -
211D GLN* 2.7 31.1 - - - +
249D ILE* 3.4 17.1 - - + +
250D HIS 2.9 6.5 - - - +
251D THR* 2.9 11.9 + - - +
60E GLY 3.7 2.5 - - - +
61E MET* 3.2 43.3 + - - +
62E GLN* 3.5 17.3 + - + +
251E THR* 3.7 4.9 - - - +
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN* 3.7 15.0 - - + +
36D GLN* 3.7 19.7 - - + +
62D GLN* 1.3 78.9 - - - +
64D ARG* 1.3 62.2 + - - +
65D TYR* 4.0 27.4 - - + +
248D PHE 3.7 0.6 - - - +
249D ILE* 3.2 7.0 - - - +
250D HIS* 2.7 36.5 + - + +
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Residues in contact with ARG 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN* 2.4 45.4 + - - +
62D GLN* 5.4 0.6 + - - -
63D ALA* 1.3 75.0 - - - +
65D TYR* 1.3 64.2 + - - +
66D SER 4.2 0.6 + - - -
247D ASP* 3.5 33.3 - - + +
248D PHE 3.6 2.5 - - - -
249D ILE* 3.1 27.0 - - + +
39E HIS* 6.1 0.4 + - - -
58E VAL* 4.7 8.6 - - - +
59E PHE* 2.8 23.0 + - - +
60E GLY* 2.7 31.9 + - - -
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Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLY* 3.4 31.2 - - - -
30D GLU* 4.5 7.2 - - - -
32D GLN* 4.3 5.4 - - + -
33D TYR* 3.4 26.4 + - + +
36D GLN* 4.5 2.4 + - - -
63D ALA* 4.0 24.3 - - + +
64D ARG* 1.3 81.2 - - - +
66D SER* 1.3 64.7 + - - +
67D LEU* 3.6 4.9 - - - +
72D PRO* 4.1 24.7 - - + -
74D LEU* 5.7 2.5 - - + -
227D ILE* 3.4 48.8 - - + +
247D ASP* 3.6 2.8 - - - -
248D PHE* 2.9 52.7 + + + +
250D HIS* 4.5 5.6 + - + -
276D PHE* 5.1 4.3 - + - -
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Residues in contact with SER 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLY* 6.0 3.0 - - - -
64D ARG 4.2 1.0 + - - -
65D TYR* 1.3 75.1 - - - +
67D LEU* 1.3 67.1 + - - +
68D ARG* 3.2 34.2 + - - +
70D GLU* 3.8 28.1 + - - +
72D PRO* 4.2 5.7 - - - +
246D GLY 3.9 0.9 - - - -
247D ASP* 3.8 16.6 + - - -
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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