Contacts of the strand formed by residues 54 - 66 (chain A) 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 GLY 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.5 23.5 - - - +
47A LYS 4.2 0.2 - - - -
48A ASP* 3.5 14.8 - - - -
52A GLY 3.5 2.6 + - - -
53A THR* 1.3 83.6 - - - +
55A THR* 1.3 62.9 + - - +
258A TYR* 4.0 0.7 - - - -
259A LEU* 3.0 28.7 + - - +
260A ASN 5.0 0.2 + - - -
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Residues in contact with THR 55 (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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46A ARG* 3.1 9.9 - - - +
47A LYS* 2.7 48.6 + - - +
49A ASP* 4.4 11.4 - - + -
53A THR 3.7 9.4 - - - +
54A GLY* 1.3 79.6 - - - +
56A LEU* 1.3 61.7 + - - +
57A SER* 4.4 0.9 - - - -
256A HIS* 3.9 19.4 - - + +
257A ILE 3.2 14.8 - - - -
258A TYR* 3.9 21.8 - - + -
259A LEU* 3.6 7.6 - - - +
175B ARG* 4.6 9.9 + - - +
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Residues in contact with LEU 56 (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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40A ILE* 3.2 35.9 - - + +
41A LEU* 3.7 32.8 - - + +
44A GLY 4.0 9.6 - - - +
45A VAL* 3.3 20.2 - - - +
46A ARG* 4.1 3.6 - - + +
55A THR* 1.3 73.3 - - - +
57A SER* 1.3 61.9 + - - +
256A HIS* 3.2 1.6 - - - -
257A ILE* 2.8 36.4 + - + +
259A LEU* 3.6 19.1 - - + -
262A ILE* 4.2 12.3 - - + -
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Residues in contact with SER 57 (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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40A ILE* 4.2 1.3 - - - -
44A GLY* 3.5 3.4 - - - -
45A VAL* 2.9 34.5 + - - +
47A LYS* 3.7 18.7 - - - +
55A THR* 4.1 3.3 - - - -
56A LEU* 1.3 75.6 - - - +
58A VAL* 1.3 66.8 + - - +
254A ASP* 3.0 24.0 + - - -
255A ALA 3.2 9.2 - - - -
256A HIS* 3.5 9.4 - - - -
202B TYR* 3.0 22.1 + - - -
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Residues in contact with VAL 58 (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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39A HIS* 4.2 16.4 - - + +
40A ILE* 3.5 23.8 - - + -
43A CYS* 4.6 2.9 - - + +
44A GLY* 3.9 19.7 - - - +
57A SER* 1.3 79.9 - - - +
59A PHE* 1.3 59.6 + - - +
60A GLY 4.4 2.5 - - - +
61A MET* 3.2 43.3 - - + -
253A GLY 3.7 0.3 - - - +
254A ASP* 3.8 2.4 - - - +
255A ALA* 2.9 28.6 + - + +
64B ARG* 5.3 2.7 - - - +
202B TYR* 4.1 5.8 - - - -
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Residues in contact with PHE 59 (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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58A VAL* 1.3 72.0 - - - +
60A GLY* 1.3 55.8 + - - +
253A GLY* 2.9 39.3 - - - -
254A ASP* 3.8 1.1 - - + -
64B ARG* 2.4 39.0 + - - +
200B GLN* 3.3 39.5 - - + -
202B TYR* 3.5 58.7 + + + -
209B SER* 4.0 9.0 - - - +
210B CYS* 3.8 6.3 - - - -
211B GLN* 3.6 35.4 - - + -
249B ILE* 3.8 18.0 - - + +
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Residues in contact with GLY 60 (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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58A VAL 4.0 1.0 + - - -
59A PHE* 1.3 70.7 - - - +
61A MET* 1.3 68.2 - - - +
252A LEU 3.2 12.1 - - - -
253A GLY 2.7 14.3 + - - -
62B GLN* 3.7 8.8 - - - +
64B ARG* 2.8 23.5 + - - -
211B GLN* 3.9 16.8 - - - -
249B ILE* 4.2 6.1 - - - -
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Residues in contact with MET 61 (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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36A GLN* 3.5 59.0 - - + +
39A HIS* 3.5 28.0 - - + -
40A ILE* 3.6 6.1 - - + -
58A VAL* 3.2 26.5 - - + -
60A GLY* 1.3 82.8 - - - +
62A GLN* 1.3 62.1 + - - +
219A MET* 5.2 1.1 - - - +
251A THR* 3.4 1.0 - - - -
252A LEU* 2.9 38.0 + - + -
255A ALA* 3.5 19.3 - - + -
62B GLN* 3.1 15.5 + - - +
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Residues in contact with GLN 62 (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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32A GLN* 4.3 4.0 - - - +
36A GLN* 3.6 8.8 + - - +
61A MET* 1.3 79.2 - - - +
63A ALA* 1.3 65.5 + - - +
64A ARG* 5.8 0.4 - - + -
211A GLN* 3.3 12.3 + - - -
249A ILE* 3.6 22.3 - - + +
250A HIS 3.2 5.8 - - - +
251A THR* 2.8 24.1 + - - +
60B GLY 3.5 4.5 - - - +
61B MET* 3.2 43.2 + - - +
62B GLN* 3.3 19.3 + - + +
251B THR* 3.6 3.4 - - - +
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Residues in contact with ALA 63 (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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32A GLN* 3.5 15.5 - - + +
36A GLN* 3.8 17.9 - - + +
62A GLN* 1.3 78.9 - - - +
64A ARG* 1.3 60.3 + - - +
65A TYR* 3.5 33.9 - - + +
248A PHE 3.7 0.7 - - - +
249A ILE* 3.3 4.6 - - - +
250A HIS* 2.7 40.8 + - + +
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Residues in contact with ARG 64 (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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29A GLY* 5.2 1.7 - - - +
32A GLN* 2.7 36.0 + - - +
62A GLN* 5.8 0.2 - - - -
63A ALA* 1.3 74.4 - - - +
65A TYR* 1.3 65.9 + - - +
66A SER 4.1 1.7 + - - +
247A ASP* 3.4 36.9 + - - +
248A PHE 3.6 2.5 - - - -
249A ILE* 3.2 26.8 - - + +
39B HIS* 6.3 0.8 - - - -
58B VAL* 4.5 9.3 - - - +
59B PHE* 2.9 24.2 + - - +
60B GLY 2.7 29.5 + - - -
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Residues in contact with TYR 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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29A GLY* 3.5 33.0 - - - -
30A GLU* 4.7 2.2 - - - -
32A GLN* 4.5 3.4 - - + -
33A TYR* 3.2 36.0 + - + +
36A GLN* 3.9 3.3 + - - -
63A ALA* 3.5 27.4 - - + +
64A ARG* 1.3 77.3 - - - +
66A SER* 1.3 63.5 + - - +
67A LEU* 3.6 0.3 + - - +
72A PRO* 4.0 32.5 - - + -
74A LEU* 5.1 3.4 - - + -
223A VAL* 5.7 0.2 - - - +
227A ILE* 3.6 28.1 - - + +
247A ASP* 3.5 2.8 - - - -
248A PHE* 2.7 64.7 + + + +
250A HIS* 4.2 10.2 - + + -
276A PHE* 4.9 2.0 - + + -
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Residues in contact with SER 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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29A GLY* 6.2 1.4 - - - -
64A ARG* 4.1 2.2 + - - +
65A TYR* 1.3 73.7 - - - +
67A LEU* 1.3 61.3 + - - +
68A ARG* 3.0 42.0 + - - +
70A GLU* 3.9 25.5 + - - +
72A PRO* 4.4 7.3 - - - +
247A ASP* 3.7 10.5 + - - -
276A PHE* 5.7 0.7 - - - -
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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