Contacts of the helix formed by residues 72 - 84 (chain A) in PDB entry 2HHL
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ARG 3.4 0.4 + - - -
71A PRO* 1.3 85.1 - - + +
73A VAL* 1.3 63.2 + - - +
74A ASP 3.3 2.2 - - - -
75A GLU* 3.5 25.7 + - + +
76A PHE* 3.0 23.4 + - - +
169A ASP 3.9 9.4 + - - -
170A THR* 4.1 14.2 - - - +
172A LEU* 4.4 1.3 - - + -
173A LEU* 3.6 53.4 - - + +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 34.1 - - + +
69A LYS* 3.5 33.4 - - + -
70A ARG 3.5 15.5 - - - +
71A PRO 3.3 3.0 + - - -
72A HIS* 1.3 77.9 - - - +
74A ASP* 1.3 64.2 + - - +
76A PHE* 3.6 1.2 - - + +
77A LEU* 2.8 46.1 + - + +
104A LEU* 3.9 13.0 - - + -
172A LEU* 3.6 23.3 - - + -
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Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 2.7 38.0 + - - -
72A HIS 3.3 0.8 - - - -
73A VAL* 1.3 79.5 - - - +
75A GLU* 1.3 57.9 + - - +
77A LEU* 3.8 1.2 - - - +
78A GLN* 2.9 41.8 + - - +
104A LEU* 4.5 5.0 - - - +
106A ARG* 4.6 8.6 + - - -
107A TRP* 3.4 33.5 - - + -
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Residues in contact with GLU 75 (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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72A HIS* 3.5 27.5 + - - +
73A VAL 3.4 0.4 - - - -
74A ASP* 1.3 74.6 - - - +
76A PHE* 1.3 67.9 + - - +
78A GLN* 3.5 9.3 + - - +
79A ARG* 3.1 23.5 + - + +
173A LEU* 3.7 18.3 - - - +
176A ILE* 3.5 21.6 - - + +
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Residues in contact with PHE 76 (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 ILE* 4.1 18.4 - - + -
39A LEU* 4.1 22.4 - - + -
72A HIS 3.0 18.4 + - - +
73A VAL 3.6 3.1 - - - +
75A GLU* 1.3 80.6 - - - +
77A LEU* 1.3 72.9 + - + +
79A ARG* 3.9 1.6 - - - +
80A MET* 3.0 63.7 + - + +
143A VAL* 4.3 10.5 - - + -
172A LEU* 3.4 40.8 - - + +
175A LEU* 3.7 35.4 - - + -
176A ILE* 4.1 14.8 - - + +
179A PHE* 4.2 2.7 - + - -
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Residues in contact with LEU 77 (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 ILE* 4.5 6.7 - - + -
39A LEU* 4.2 9.9 - - + -
73A VAL* 2.8 29.7 + - + +
74A ASP* 3.9 2.7 - - - +
76A PHE* 1.3 89.9 - - + +
78A GLN* 1.3 59.0 + - - +
80A MET* 3.8 1.7 - - - -
81A GLY 2.8 26.5 + - - -
104A LEU* 3.9 45.8 - - + +
105A ASP* 4.8 3.1 - - + -
107A TRP* 4.5 10.8 - - + -
109A VAL* 3.3 21.3 - - + +
110A PHE* 3.8 32.3 - - + -
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Residues in contact with GLN 78 (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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74A ASP* 2.9 25.6 + - - +
75A GLU* 3.8 8.6 - - - +
76A PHE 3.3 0.2 - - - -
77A LEU* 1.3 77.5 - - - +
79A ARG* 1.3 59.9 + - - +
81A GLY* 3.5 2.3 + - - -
82A GLN* 3.3 28.2 + - - +
107A TRP* 3.4 50.3 - - + +
109A VAL* 4.4 6.3 - - + +
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Residues in contact with ARG 79 (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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75A GLU* 3.1 16.2 + - + +
76A PHE 3.9 2.2 - - - +
78A GLN* 1.3 73.2 - - - +
80A MET* 1.3 67.9 + - + +
82A GLN* 2.8 50.3 + - - +
83A LEU* 3.3 51.4 + - + +
176A ILE* 3.8 28.3 - - + +
180A GLU* 2.9 31.0 + - + +
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Residues in contact with MET 80 (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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31A VAL* 3.6 30.1 - - + -
33A ILE* 4.5 5.4 - - + -
76A PHE* 3.0 48.9 + - + +
77A LEU* 3.9 5.6 - - - +
79A ARG* 1.3 78.4 - - + +
81A GLY* 1.3 57.6 + - - +
83A LEU* 3.2 1.4 + - - -
84A PHE* 2.9 57.6 + - + -
86A CYS* 3.3 19.0 - - - -
109A VAL* 5.2 0.2 - - + -
175A LEU 5.4 0.2 - - - +
176A ILE* 5.9 2.9 - - - -
179A PHE* 3.6 41.3 - - + -
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Residues in contact with GLY 81 (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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28A LYS* 5.1 3.8 + - - -
77A LEU 2.8 17.1 + - - -
78A GLN 3.8 2.9 - - - -
80A MET* 1.3 75.5 - - - +
82A GLN* 1.3 58.5 + - - +
84A PHE 4.1 8.2 - - - +
86A CYS* 3.8 5.5 - - - -
109A VAL* 3.8 28.2 - - - +
111A ARG* 4.6 10.0 + - - -
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Residues in contact with GLN 82 (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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28A LYS* 4.4 12.7 + - - -
78A GLN* 3.3 14.3 + - - +
79A ARG* 2.8 54.0 + - - +
81A GLY* 1.3 76.7 - - - +
83A LEU* 1.3 63.0 + - + +
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Residues in contact with LEU 83 (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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28A LYS* 3.7 20.7 - - - +
79A ARG* 3.3 47.7 + - + +
80A MET* 3.2 2.1 + - - -
82A GLN* 1.3 82.6 - - + +
84A PHE* 1.3 93.0 + - + +
179A PHE* 4.2 1.8 - - + +
180A GLU* 4.0 28.0 - - + +
183A SER* 3.6 32.2 + - - +
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Residues in contact with PHE 84 (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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28A LYS* 4.0 10.9 - - - +
29A LYS* 3.5 28.0 - - + +
31A VAL* 3.5 20.6 - - + -
80A MET* 2.9 54.8 + - + +
81A GLY* 4.1 9.5 - - - +
83A LEU* 1.3 104.6 - - + +
85A GLU* 1.3 64.7 + - - +
86A CYS* 3.4 9.8 + - - -
109A VAL 5.4 0.3 - - - +
111A ARG* 4.5 7.1 + - - -
179A PHE* 3.4 37.2 - + + -
182A LEU* 4.1 14.6 - - + -
183A SER* 4.3 10.1 - - - -
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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