Contacts of the helix formed by residues 45 - 56 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88I LYS* 3.3 50.3 + - + +
33J TRP* 4.1 14.9 - + + -
36J VAL* 3.7 31.2 - - + +
41J GLN* 2.8 27.2 + - - +
42J ILE* 2.9 11.6 + - - +
44J PRO* 1.3 76.8 - - - +
46J LEU* 1.3 57.9 + - - +
47J ASP 3.3 2.5 - - - -
48J GLN* 3.0 32.5 + - - +
49J LEU* 2.9 28.7 + - - +
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Residues in contact with LEU 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J ILE* 3.1 26.8 + - + +
43J GLN* 3.3 24.3 + - + +
44J PRO 3.4 0.4 - - - -
45J HIS* 1.3 78.8 - - - +
47J ASP* 1.3 65.2 + - - +
49J LEU* 3.1 11.1 + - + -
50J ASN* 2.9 20.8 + - - +
76J ALA* 4.4 8.5 - - + -
79J LEU* 4.0 21.1 - - + -
80J ILE* 4.4 9.4 - - + -
83J LEU* 4.0 27.6 - - + -
97J TYR* 4.3 15.3 - - + +
100J ILE* 3.4 27.4 - - + +
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Residues in contact with ASP 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I SER* 3.7 16.1 - - - +
93I THR* 4.7 8.3 + - - +
96I THR* 3.5 39.0 + - - +
97I TYR* 4.7 10.0 + - - -
44J PRO 4.9 4.2 + - - +
45J HIS* 3.3 0.6 - - - +
46J LEU* 1.3 78.5 - - - +
48J GLN* 1.3 63.5 + - - +
50J ASN* 3.4 7.3 + - - +
51J LEU* 3.1 22.0 + - - +
96J THR* 4.9 0.7 - - - +
97J TYR* 3.8 21.2 + - - -
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Residues in contact with GLN 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I LYS* 4.5 4.5 + - + +
89I ASP* 3.7 32.6 + - + +
92I SER* 3.2 19.6 - - - +
33J TRP* 4.1 14.4 - - + -
44J PRO 5.5 0.2 + - - -
45J HIS* 3.0 41.9 + - + +
47J ASP* 1.3 77.4 - - - +
49J LEU* 1.3 59.0 + - - +
51J LEU* 3.3 3.8 + - + +
52J VAL* 2.9 35.7 + - + +
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Residues in contact with LEU 49 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J TRP* 3.9 17.0 - - + -
42J ILE* 5.2 3.4 - - + -
45J HIS 2.9 13.8 + - - +
46J LEU* 3.1 20.8 + - + +
48J GLN* 1.3 73.9 - - - +
50J ASN* 1.3 58.3 + - - +
52J VAL* 3.2 3.5 + - + +
53J LEU* 3.0 53.7 + - + +
59J ILE* 3.4 36.8 - - + -
72J VAL* 4.0 19.1 - - + -
76J ALA* 4.4 4.0 - - + -
100J ILE* 4.0 17.5 - - + -
103J TRP* 4.3 14.6 - - + -
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Residues in contact with ASN 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I THR* 5.9 3.5 - - - +
96I THR* 5.5 2.9 + - - +
46J LEU 2.9 13.0 + - - +
47J ASP* 3.5 12.6 - - - +
49J LEU* 1.3 76.9 - - - +
51J LEU* 1.3 58.1 + - - +
53J LEU 3.3 0.3 + - - -
54J ARG 3.0 21.7 + - - -
95J THR 5.4 0.3 - - - +
96J THR 3.2 23.6 - - - +
97J TYR* 3.3 13.3 - - + +
98J ARG 4.3 0.5 + - - -
99J HIS* 2.9 58.4 - - - +
100J ILE* 3.1 20.9 - - + +
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Residues in contact with LEU 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I ASP* 3.9 4.9 - - - +
91I LYS* 4.1 21.8 - - + +
92I SER* 3.2 38.1 - - - +
95I THR* 4.5 17.7 - - + +
47J ASP 3.1 13.6 + - - +
48J GLN* 3.3 7.6 + - + +
50J ASN* 1.3 76.0 - - - +
52J VAL* 1.3 67.7 + - + +
54J ARG* 3.1 52.2 + - - +
55J ASP* 3.8 7.8 + - - +
99J HIS* 5.2 0.4 - - - -
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Residues in contact with VAL 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J GLN* 5.5 2.5 - - - +
33J TRP* 4.2 18.6 - - + +
48J GLN* 2.9 26.7 + - + +
49J LEU* 3.2 9.2 + - + +
51J LEU* 1.3 77.7 - - + +
53J LEU* 1.3 61.6 + - + +
55J ASP 3.2 0.3 + - - -
56J ASN* 2.8 47.3 + - + +
59J ILE* 3.5 39.9 - - + +
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Residues in contact with LEU 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J LEU* 3.0 44.0 + - + +
51J LEU 3.2 0.2 - - - -
52J VAL* 1.3 73.5 - - + +
54J ARG* 1.3 66.5 + - - +
55J ASP 3.3 0.4 - - - -
56J ASN 3.2 15.5 - - - +
57J THR 4.0 3.4 - - - +
58J PHE 4.2 0.7 - - - -
59J ILE* 4.1 19.7 - - + +
99J HIS* 3.6 21.5 - - + +
100J ILE* 3.9 11.2 - - - -
102J ARG* 2.8 31.2 + - - +
103J TRP* 3.6 52.3 - - + +
102L ARG* 4.1 0.2 - - - -
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Residues in contact with ARG 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I LYS* 4.1 8.9 - - - +
95I THR* 4.4 10.0 - - - +
98I ARG* 4.4 5.9 - - - +
2005I SO4 3.3 18.6 + - - -
50J ASN 3.0 5.6 + - - +
51J LEU* 3.3 33.2 - - - +
52J VAL 3.1 0.6 - - - -
53J LEU* 1.3 81.1 - - - +
55J ASP* 1.3 88.2 + - - +
99J HIS* 3.5 42.1 + - + +
98L ARG* 3.2 61.6 - - + +
99L HIS* 4.6 9.9 + - + -
102L ARG* 3.8 16.6 + - - +
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Residues in contact with ASP 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J LEU* 4.3 6.1 - - - +
52J VAL 3.2 2.5 + - - +
54J ARG* 1.3 122.0 + - - +
56J ASN* 1.3 75.0 + - - +
98L ARG* 3.8 13.6 + - - +
102L ARG* 3.8 20.4 - - - +
105L ASP* 4.7 7.8 - - - +
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Residues in contact with ASN 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J GLN* 5.9 0.2 - - - -
52J VAL* 2.8 35.7 + - + +
53J LEU* 3.2 9.5 - - - +
54J ARG 3.6 0.4 - - - -
55J ASP* 1.3 93.2 - - - +
57J THR* 1.3 61.5 - - - +
58J PHE 3.3 18.6 - - - +
61J SER* 2.7 30.1 + - - +
102J ARG* 2.8 19.8 + - - -
102L ARG* 3.9 3.4 - - - -
105L ASP* 5.2 4.2 - - - +
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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