Contacts of the helix formed by residues 56 - 65 (chain A) in PDB entry 3HH2
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 PRO 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LYS 3.8 7.2 - - - +
55A TYR* 1.3 83.8 - - + +
57A HIS* 1.3 63.7 + - - +
58A THR 3.1 0.7 + - - -
59A HIS* 3.4 7.6 + - + +
60A LEU* 3.4 22.8 + - - +
29B TRP* 4.8 2.9 - - + -
99B PRO 3.5 22.9 - - - +
100B ALA* 3.6 10.1 - - + +
101B MET* 3.7 20.2 - - - -
51D ILE* 3.5 44.6 - - + +
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Residues in contact with HIS 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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55A TYR* 3.1 0.6 - - + -
56A PRO* 1.3 79.1 - - - +
58A THR* 1.3 67.0 + - - +
60A LEU* 3.2 10.8 + - + +
61A VAL* 3.1 42.0 + - + +
38B TYR* 4.8 0.2 - - - -
40B ALA* 3.2 20.5 + - + -
41B ASN 2.7 24.5 + - - -
42B TYR* 4.3 4.0 - - - -
43B CYS 5.5 0.7 - - - -
76B PRO* 4.7 7.0 - - + +
79B MET* 3.4 15.3 - - + +
100B ALA 3.3 19.7 + - - +
101B MET* 3.1 25.8 - - - +
103B VAL* 3.0 27.1 - - + +
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Residues in contact with THR 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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53A GLN* 3.4 32.3 - - - +
55A TYR* 3.2 22.8 + - - +
56A PRO 3.1 1.6 + - - -
57A HIS* 1.3 84.6 + - - +
59A HIS* 1.3 62.7 + - - +
61A VAL* 3.5 5.3 + - - +
62A HIS* 3.2 18.1 + - + +
72A PRO* 3.8 11.4 - - + -
108A CYS 4.3 1.9 + - - -
109A SER* 3.7 36.9 - - - -
76B PRO* 6.0 1.6 - - - +
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Residues in contact with HIS 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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49A PHE* 4.0 23.0 + + - -
50A VAL* 3.4 28.2 - - + +
53A GLN* 3.6 8.0 + - - +
55A TYR 5.7 0.2 - - - +
56A PRO* 3.4 8.5 + - + +
58A THR* 1.3 76.7 - - - +
60A LEU* 1.3 61.2 + - + +
62A HIS* 3.2 25.8 + + - +
63A GLN* 2.9 50.8 + - + +
29B TRP* 6.0 2.9 - + + -
43D ASP* 5.5 1.4 + - - -
47D PHE* 3.4 35.8 - + + -
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Residues in contact with LEU 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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56A PRO 3.4 15.8 + - - +
57A HIS* 3.2 8.6 + - - +
59A HIS* 1.3 79.7 - - + +
61A VAL* 1.3 62.4 + - + +
63A GLN* 3.4 2.8 + - - -
64A ALA* 3.2 19.6 + - - +
22B VAL* 4.3 20.9 - - + +
24B PHE* 4.7 0.9 - - + -
27B PHE* 3.5 35.9 - - + -
29B TRP* 3.6 40.2 - - + +
38B TYR* 3.5 28.0 - - + +
40B ALA* 5.7 1.1 - - + -
101B MET* 3.9 21.1 - - + -
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Residues in contact with VAL 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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57A HIS* 3.1 45.7 + - + +
58A THR* 3.8 7.4 - - - +
60A LEU* 1.3 75.0 - - + +
62A HIS* 1.3 58.9 + - - +
64A ALA* 3.2 1.6 + - - -
65A ASN* 2.8 25.8 + - - -
66A PRO* 3.4 8.3 - - + +
69A SER* 4.1 21.5 + - - -
70A ALA 6.1 0.2 - - - +
20B LEU* 4.2 13.0 - - + -
40B ALA* 5.4 0.7 - - + -
41B ASN 3.7 9.9 - - - +
42B TYR* 3.8 18.6 - - + -
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Residues in contact with HIS 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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49A PHE 6.1 0.7 - - - -
58A THR* 3.2 10.7 + - + +
59A HIS* 3.2 32.3 + + - +
61A VAL* 1.3 81.2 - - - +
63A GLN* 1.3 65.5 + - - +
65A ASN* 3.1 18.4 + - - +
69A SER* 5.8 1.3 - - - -
71A GLY* 4.5 10.5 - - - -
72A PRO* 4.2 25.8 - - + +
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Residues in contact with GLN 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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59A HIS* 2.9 49.9 + - + +
60A LEU* 3.7 2.9 - - - +
61A VAL 3.3 0.2 - - - -
62A HIS* 1.3 74.8 + - - +
64A ALA* 1.3 62.2 + - - +
65A ASN* 3.4 3.6 + - - +
27B PHE* 3.3 51.9 + - + +
29B TRP* 4.5 6.1 + - - -
44D ASN* 4.4 7.6 - - - +
47D PHE* 4.0 10.4 - - - -
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Residues in contact with ALA 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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60A LEU 3.2 11.2 + - - +
61A VAL 3.7 6.5 - - - +
63A GLN* 1.3 79.2 - - - +
65A ASN* 1.3 70.3 + - - +
66A PRO* 3.3 2.7 - - + +
20B LEU* 4.0 32.1 - - + -
21B THR 5.5 0.4 - - - +
27B PHE* 3.8 18.3 - - + -
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Residues in contact with ASN 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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61A VAL 2.8 11.2 + - - -
62A HIS* 3.1 14.7 + - - +
63A GLN 4.1 3.4 - - - +
64A ALA* 1.3 80.3 - - - +
66A PRO* 1.3 64.9 - - - +
69A SER* 3.7 15.0 + - - +
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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