Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 1H48
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 ASP 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP* 3.5 11.0 - - - +
70A GLY 3.7 1.6 + - - -
71A ALA* 1.3 71.0 - - - +
73A SER* 1.3 59.5 + - - +
74A ARG* 3.0 36.6 + - - +
75A GLU* 2.9 54.2 + - + +
76A LEU* 3.4 6.9 + - - +
78A ARG* 4.6 4.7 + - - -
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Residues in contact with SER 73 (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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35A SER* 3.7 4.2 + - - -
36A ASP* 2.7 32.7 + - - -
38A ASP* 3.7 16.3 - - - +
41A LEU* 4.2 11.3 - - - +
42A HIS* 2.7 33.1 + - - -
45A THR* 5.0 1.2 + - - -
71A ALA 3.2 1.6 + - - -
72A ASP* 1.3 71.4 - - - +
74A ARG* 1.3 58.2 + - - +
76A LEU* 3.5 12.8 + - - +
77A LEU* 3.0 26.0 + - - +
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Residues in contact with ARG 74 (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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22A GLY* 4.0 22.0 + - - -
41A LEU* 3.4 19.5 - - + -
72A ASP* 3.0 19.9 + - - +
73A SER* 1.3 77.7 - - - +
75A GLU* 1.3 57.8 + - - +
77A LEU* 3.3 5.7 + - - +
78A ARG* 2.9 51.4 + - - +
115A PHE* 3.3 49.6 + - - +
118A GLU* 4.6 9.7 + - - +
119A ASP* 2.8 41.9 + - - +
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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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71A ALA* 4.7 5.8 - - + +
72A ASP* 2.9 37.9 + - + +
74A ARG* 1.3 75.4 - - - +
76A LEU* 1.3 56.4 + - + +
78A ARG* 3.1 27.5 + - - +
79A GLU* 2.8 35.8 + - - +
82A ARG* 5.1 1.6 + - - +
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Residues in contact with LEU 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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35A SER* 4.9 2.0 - - - -
42A HIS* 4.8 3.4 - - + +
45A THR* 4.8 4.3 - - + +
57A ILE* 5.9 2.7 - - + -
61A PHE* 3.6 49.6 - - + -
68A PHE* 4.2 18.2 - - + -
71A ALA* 4.6 15.5 - - + -
72A ASP 3.4 8.0 + - - +
73A SER* 3.6 22.2 - - - +
75A GLU* 1.3 77.9 - - + +
77A LEU* 1.3 59.7 + - - +
79A GLU* 3.4 2.4 + - + -
80A ALA* 2.8 31.9 + - - +
201A CDI 4.2 32.5 - - + -
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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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41A LEU* 4.3 18.2 - - + +
44A LEU* 4.2 20.0 - - + -
45A THR* 3.4 29.8 + - + +
48A LEU* 3.7 29.6 - - + -
73A SER 3.0 14.9 + - - +
74A ARG* 3.3 8.7 + - - +
76A LEU* 1.3 76.3 - - - +
78A ARG* 1.3 58.1 + - - +
80A ALA* 3.3 1.2 + - - +
81A TRP* 2.9 29.3 + - - +
116A ILE* 4.8 5.2 - - + -
119A ASP* 3.8 28.9 - - + +
120A LEU* 4.2 12.6 - - + -
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Residues in contact with ARG 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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72A ASP* 4.6 5.1 + - - -
74A ARG* 2.9 42.0 + - - +
75A GLU* 3.6 31.9 - - - +
77A LEU* 1.3 74.7 - - - +
79A GLU* 1.3 64.8 + - - +
81A TRP* 3.3 7.3 + - - +
82A ARG* 3.0 51.2 + - - +
118A GLU 5.6 0.2 - - - -
119A ASP* 2.9 54.8 + - - +
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Residues in contact with GLU 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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61A PHE* 3.8 24.0 - - + -
75A GLU 2.8 19.7 + - - +
76A LEU* 3.8 5.4 - - + +
78A ARG* 1.3 69.6 - - - +
80A ALA* 1.3 65.9 + - - +
82A ARG* 2.8 41.4 + - - +
83A ARG* 2.7 57.5 + - - +
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Residues in contact with ALA 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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45A THR* 3.5 26.9 - - + -
48A LEU* 6.0 0.4 - - + -
49A LEU* 3.9 16.4 - - + +
60A LEU* 4.4 8.1 - - - -
61A PHE* 4.1 10.9 - - + -
76A LEU 2.8 22.1 + - - +
77A LEU* 3.6 3.8 - - + +
79A GLU* 1.3 73.0 - - - +
81A TRP* 1.3 57.5 + - - +
83A ARG* 3.2 3.3 + - - +
84A ILE* 3.0 36.4 + - + +
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Residues in contact with TRP 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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48A LEU* 4.1 10.7 - - + +
77A LEU* 2.9 17.7 + - + +
78A ARG* 3.7 7.9 - - - +
79A GLU 3.2 0.2 - - - -
80A ALA* 1.3 78.0 - - - +
82A ARG* 1.3 57.4 + - + +
84A ILE* 3.3 32.0 + - + +
85A GLN* 2.9 72.2 + - + +
89A TYR 4.5 1.1 - - - -
90A THR* 4.0 5.8 - - - -
91A LEU* 3.7 43.5 - - + -
119A ASP 3.8 17.0 - - - +
120A LEU* 3.3 45.1 + - + -
154A LEU* 3.9 13.2 - - + -
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Residues in contact with ARG 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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75A GLU* 5.1 1.4 + - - +
78A ARG* 3.0 43.6 + - - +
79A GLU* 2.8 52.8 + - - +
81A TRP* 1.3 76.5 - - + +
83A ARG* 1.3 58.4 + - + +
85A GLN* 3.5 10.1 + - - +
86A ALA* 2.9 28.1 + - - +
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Residues in contact with ARG 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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54A LEU* 3.8 18.7 - - + +
60A LEU* 3.5 48.1 + - + +
61A PHE* 4.7 4.7 - - - -
79A GLU* 2.7 44.2 + - - +
80A ALA* 3.5 8.7 - - - +
82A ARG* 1.3 77.2 - - + +
84A ILE* 1.3 66.4 + - - +
86A ALA* 3.6 9.1 + - + +
87A LYS* 3.6 17.3 + - - +
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Residues in contact with ILE 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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48A LEU* 3.6 38.8 - - + -
49A LEU* 3.9 8.5 - - + +
52A ALA* 4.0 5.6 - - + -
54A LEU* 3.8 20.2 - - + -
80A ALA* 3.0 29.7 + - + +
81A TRP* 3.3 29.4 + - + +
83A ARG* 1.3 75.2 - - - +
85A GLN* 1.3 65.2 + - - +
87A LYS* 3.1 18.9 + - - +
89A TYR* 3.5 33.2 + - + -
154A LEU* 3.7 13.0 - - + -
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Residues in contact with GLN 85 (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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81A TRP* 2.9 60.5 + - + +
82A ARG* 3.8 9.2 - - - +
84A ILE* 1.3 75.0 - - - +
86A ALA* 1.3 55.4 + - - +
88A GLY* 2.7 25.3 + - - -
89A TYR 3.5 22.6 + - - +
90A THR* 5.0 5.5 + - - +
120A LEU 5.5 0.2 + - - -
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Residues in contact with ALA 86 (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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82A ARG 2.9 18.9 + - - +
83A ARG* 3.8 10.1 - - - +
84A ILE 3.2 0.2 - - - -
85A GLN* 1.3 75.5 - - - +
87A LYS* 1.3 59.6 + - + +
88A GLY* 3.4 1.0 + - - -
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Residues in contact with LYS 87 (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 ALA 3.1 21.3 + - - +
53A ALA 4.3 1.8 + - - -
54A LEU* 3.5 35.1 - - + +
83A ARG 3.6 8.5 + - - +
84A ILE 3.1 10.7 + - - +
85A GLN 3.1 0.8 - - - -
86A ALA* 1.3 77.3 - - + +
88A GLY* 1.3 57.3 + - - +
89A TYR* 3.6 22.7 + - + -
156A LYS 5.2 1.9 - - - +
125B ASP* 3.1 29.7 + - - -
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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