Contacts of the helix formed by residues 45 - 56 (chain A) in PDB entry 2HQT
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 HIS 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A TRP* 3.9 18.2 - + + -
36A VAL* 3.9 27.7 - - + +
41A GLN* 2.8 45.8 + - + +
42A ILE* 2.9 13.4 + - - +
44A PRO* 1.3 75.5 - - - +
46A LEU* 1.3 58.5 + - - +
47A ASP 3.4 2.5 - - - -
48A GLN* 3.1 34.7 + - - +
49A LEU* 3.0 26.7 + - - +
88B LYS* 3.6 31.7 + - + +
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Residues in contact with LEU 46 (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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42A ILE* 3.0 27.3 + - + +
43A GLN* 3.1 22.7 + - + +
45A HIS* 1.3 73.0 - - - +
47A ASP* 1.3 62.7 + - - +
49A LEU* 3.1 10.5 + - + -
50A ASN* 2.7 31.9 + - - +
76A ALA* 4.9 3.8 - - + -
79A LEU* 3.7 19.1 - - + -
80A ILE* 4.4 13.2 - - + -
83A LEU* 3.6 31.9 - - + -
97A TYR* 3.9 18.4 - - + +
100A ILE* 3.4 21.7 - - + +
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Residues in contact with ASP 47 (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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43A GLN 4.9 0.4 + - - -
44A PRO 4.9 4.6 + - - +
45A HIS 3.4 0.6 - - - -
46A LEU* 1.3 77.0 - - - +
48A GLN* 1.3 58.6 + - - +
50A ASN* 3.3 7.1 + - - +
51A LEU* 2.9 27.5 + - - +
96A THR* 4.9 0.7 - - - +
97A TYR* 3.8 21.0 + - - -
92B SER* 3.7 15.6 - - - +
93B THR* 4.7 8.8 + - - +
95B THR* 5.6 0.2 + - - -
96B THR* 3.4 42.1 + - - +
97B TYR* 4.6 9.9 + - - -
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Residues in contact with GLN 48 (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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33A TRP* 3.8 22.2 + - - -
44A PRO 5.5 0.6 + - - +
45A HIS* 3.1 41.2 + - - +
47A ASP* 1.3 76.0 - - - +
49A LEU* 1.3 54.7 + - - +
51A LEU* 3.1 3.2 + - + +
52A VAL* 2.8 48.0 + - + +
88B LYS* 5.0 4.1 + - + +
89B ASP* 4.2 24.2 - - + +
92B SER* 3.3 18.9 - - - +
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Residues in contact with LEU 49 (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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33A TRP* 3.9 26.6 - - + -
42A ILE* 5.3 2.5 - - + -
45A HIS 3.0 14.4 + - - +
46A LEU* 3.5 15.0 - - + +
48A GLN* 1.3 73.9 - - - +
50A ASN* 1.3 62.8 + - - +
52A VAL* 3.3 4.0 + - + +
53A LEU* 3.0 42.7 + - + +
59A ILE* 3.6 31.9 - - + -
72A VAL* 3.8 21.8 - - + -
76A ALA* 4.4 9.6 - - + -
100A ILE* 3.9 18.4 - - + -
103A TRP* 4.2 13.0 - - + -
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Residues in contact with ASN 50 (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 LEU 2.7 15.5 + - - +
47A ASP* 3.5 8.5 - - - +
49A LEU* 1.3 78.5 - - - +
51A LEU* 1.3 61.2 + - - +
53A LEU 3.4 0.2 + - - -
54A ARG 3.1 17.3 + - - -
95A THR 5.4 0.2 - - - +
96A THR 3.3 23.0 - - - +
97A TYR* 3.2 13.6 - - + +
98A ARG 4.3 0.5 + - - -
99A HIS* 3.0 52.9 - - - +
100A ILE* 3.1 22.4 - - + +
96B THR* 5.4 2.9 + - - +
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Residues in contact with LEU 51 (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 ASP 2.9 9.6 + - - +
48A GLN* 3.6 3.1 - - + +
50A ASN* 1.3 73.2 - - - +
52A VAL* 1.3 68.1 + - + +
54A ARG* 3.3 58.0 - - - +
55A ASP* 3.7 7.2 + - - +
99A HIS* 5.4 0.4 - - - -
89B ASP* 4.1 3.8 - - - +
91B LYS* 3.7 35.0 - - + -
92B SER* 3.1 35.4 - - - +
95B THR* 4.4 12.6 - - + +
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Residues in contact with VAL 52 (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 GLN* 5.8 1.6 - - - +
33A TRP* 4.6 12.6 - - + +
48A GLN* 2.8 38.0 + - + +
49A LEU* 3.7 6.5 - - - +
51A LEU* 1.3 74.0 - - + +
53A LEU* 1.3 60.1 - - + +
55A ASP* 3.2 3.3 + - - -
56A ASN* 2.9 46.1 + - + +
59A ILE* 3.4 38.6 - - + +
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Residues in contact with LEU 53 (chain A).
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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49A LEU* 3.0 43.0 + - + +
52A VAL* 1.3 71.5 - - - +
54A ARG* 1.3 60.5 + - - +
55A ASP 3.1 1.8 - - - -
56A ASN 3.2 17.2 + - - +
57A THR 4.0 2.7 - - - +
58A PHE 4.1 1.1 - - - +
59A ILE* 4.0 23.3 - - + +
99A HIS* 3.7 15.5 - - + +
100A ILE* 3.9 11.2 - - - -
102A ARG* 2.7 40.8 + - - +
103A TRP* 3.7 51.1 - - + -
102C ARG* 3.8 0.3 - - - -
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Residues in contact with ARG 54 (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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50A ASN 3.1 7.3 + - - +
51A LEU* 3.3 34.4 - - - +
53A LEU* 1.3 81.9 - - - +
55A ASP* 1.3 90.6 + - - +
99A HIS* 3.5 39.9 - - + +
102A ARG* 4.4 0.9 + - - -
91B LYS* 4.7 6.5 - - - +
95B THR* 4.7 3.0 - - - +
98B ARG* 4.4 5.3 - - - +
2001B SO4 3.3 28.9 + - - -
98C ARG* 3.4 54.2 - - + +
99C HIS* 4.7 5.6 + - + -
102C ARG* 3.8 15.9 + - - +
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Residues in contact with ASP 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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51A LEU* 4.2 6.0 - - - +
52A VAL* 3.2 4.2 + - - +
54A ARG* 1.3 125.7 + - - +
56A ASN* 1.3 73.4 + - - +
98C ARG* 4.4 10.4 + - - +
102C ARG* 3.8 20.4 - - - +
105C ASP* 4.4 9.5 - - - +
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Residues in contact with ASN 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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52A VAL* 2.9 32.6 + - + +
53A LEU* 3.2 9.5 - - - +
54A ARG 3.6 0.8 - - - -
55A ASP* 1.3 92.8 + - - +
57A THR* 1.3 65.8 + - - +
58A PHE 3.3 18.1 + - - +
61A SER* 3.0 29.9 + - - +
102A ARG* 3.1 14.0 + - - -
102C ARG* 3.9 4.3 - - - -
105C ASP* 4.8 7.7 + - - -
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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