Contacts of the helix formed by residues 57 - 72 (chain A) in PDB entry 1MHQ
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A THR 3.8 6.1 - - - +
56A ASP* 1.3 93.8 - - - +
58A ASN* 1.3 67.0 + - - +
59A GLY 3.2 0.2 - - - -
60A PRO* 3.3 13.2 - - + +
61A THR* 4.2 7.3 + - - +
96A LYS* 5.8 6.9 + - - +
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Residues in contact with ASN 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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26A LEU* 4.9 2.2 - - + -
56A ASP* 2.8 22.5 + - - +
57A PRO* 1.3 85.2 - - - +
59A GLY* 1.3 66.7 + - - +
61A THR* 3.0 11.4 + - - -
62A HIS* 2.8 56.0 + - + +
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Residues in contact with GLY 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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26A LEU* 3.6 19.7 - - - +
53A VAL* 3.9 16.6 - - - -
56A ASP* 3.0 15.7 + - - -
58A ASN* 1.3 77.4 - - - +
60A PRO* 1.3 60.8 - - - +
63A ALA* 2.8 37.3 + - - +
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Residues in contact with PRO 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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53A VAL* 3.5 13.0 - - + +
54A ASN* 5.7 0.9 - - - +
56A ASP 3.5 8.3 - - - +
57A PRO* 3.3 18.4 - - + +
59A GLY* 1.3 87.2 - - - +
61A THR* 1.3 60.7 + - + +
64A PRO* 2.9 26.5 - - - +
96A LYS* 3.8 44.0 - - + +
97A PHE* 4.1 19.4 - - + +
100A GLU* 3.4 14.4 - - + +
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Residues in contact with THR 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 PRO 4.2 4.2 + - - +
58A ASN* 3.0 15.1 + - - -
60A PRO* 1.3 80.9 - - + +
62A HIS* 1.3 75.8 + - - +
64A PRO* 4.7 0.7 - - - -
65A TRP* 2.9 28.2 + - - +
100A GLU* 4.5 19.5 - - - +
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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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26A LEU* 4.5 10.1 - - + -
27A GLU* 5.7 5.6 - - - +
58A ASN* 2.8 49.1 + - + +
61A THR* 1.3 96.3 + - - +
63A ALA* 1.3 65.5 + - - +
64A PRO* 3.3 3.1 - - - -
65A TRP* 3.1 18.8 + - - +
66A LEU* 3.1 21.8 + - + +
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Residues in contact with ALA 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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26A LEU* 4.6 2.0 - - + +
49A PHE* 3.8 23.1 - - + -
53A VAL* 3.9 14.6 - - + -
59A GLY* 2.8 26.8 + - - +
62A HIS* 1.3 73.6 - - - +
64A PRO* 1.3 65.4 - - + +
66A LEU* 3.1 13.6 + - - +
67A LEU* 2.8 28.5 + - - +
97A PHE* 4.0 9.0 - - + -
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Residues in contact with PRO 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 PRO 2.9 29.4 - - - +
61A THR 4.3 0.2 - - - -
62A HIS 3.4 0.2 - - - -
63A ALA* 1.3 90.5 - - + +
65A TRP* 1.3 78.6 + - + +
67A LEU* 3.3 5.6 + - + +
68A ALA* 2.7 30.1 + - - +
97A PHE* 3.8 15.7 - - + -
100A GLU* 4.2 12.8 - - + -
101A VAL* 4.5 5.4 - - + -
106A PHE* 3.3 34.0 - - + -
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Residues in contact with TRP 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 THR* 2.9 29.2 + - - +
62A HIS* 3.1 8.6 + - - +
64A PRO* 1.3 86.9 - - + +
66A LEU* 1.3 67.2 + - - +
68A ALA* 3.6 3.7 - - + +
69A HIS* 3.0 24.8 + - - +
100A GLU* 4.8 8.2 + - - -
105A ARG* 3.9 31.6 - - + -
106A PHE* 3.8 45.5 - + + -
109A GLU* 4.1 12.8 - - + -
74B PRO* 3.8 9.5 - - + +
122B TRP* 3.6 42.6 - + + +
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Residues in contact with LEU 66 (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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26A LEU* 4.2 22.7 - - + -
27A GLU* 4.2 22.4 - - + +
30A LEU* 3.4 22.6 - - + +
49A PHE* 4.9 1.8 - - + -
62A HIS* 3.1 24.5 + - + +
63A ALA* 3.1 15.3 + - - +
65A TRP* 1.3 77.3 - - - +
67A LEU* 1.3 61.4 + - - +
69A HIS* 3.7 2.8 + - - +
70A LYS* 3.2 27.2 + - - +
74B PRO* 3.8 22.4 - - + +
75B GLN* 3.6 34.7 + - + +
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Residues in contact with LEU 67 (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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30A LEU* 3.8 13.9 - - + -
49A PHE* 4.1 17.3 - - + -
63A ALA 2.8 19.0 + - - +
64A PRO* 3.5 6.1 - - + +
66A LEU* 1.3 75.9 - - - +
68A ALA* 1.3 65.2 + - - +
70A LYS* 3.2 5.2 + - - +
71A ILE* 2.9 35.3 + - + +
82A ALA* 4.0 15.4 - - + +
85A VAL* 3.7 31.0 - - + -
86A LEU* 4.0 22.7 - - + +
89A CYS* 5.0 1.1 - - - -
97A PHE* 3.9 28.3 - - + -
106A PHE* 5.1 1.8 - - + -
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Residues in contact with ALA 68 (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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64A PRO 2.7 21.7 + - - +
65A TRP* 3.6 7.9 - - + +
67A LEU* 1.3 74.1 - - - +
69A HIS* 1.3 62.5 + - - +
71A ILE* 3.4 10.4 + - - +
72A GLN* 3.2 28.9 + - - +
106A PHE* 4.2 9.8 - - + -
109A GLU* 4.1 20.9 - - + -
110A LEU* 6.2 0.7 - - - -
122B TRP* 3.8 21.1 - - + -
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Residues in contact with HIS 69 (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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65A TRP 3.0 11.4 + - - +
66A LEU 3.9 4.3 - - - +
67A LEU 3.2 0.2 - - - -
68A ALA* 1.3 76.5 - - - +
70A LYS* 1.3 71.2 + - - +
72A GLN* 3.2 13.3 + - - +
73A SER 3.4 0.3 + - - -
78A GLU* 5.7 1.1 - - - -
69B HIS* 2.8 78.9 + + - -
70B LYS* 4.8 1.1 - - + -
72B GLN* 3.7 18.4 - - + -
73B SER* 3.3 26.6 + - - -
74B PRO* 3.3 25.5 - - + +
75B GLN* 6.1 0.6 + - - -
78B GLU* 4.0 9.4 + - - -
122B TRP* 3.7 18.1 - + + -
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Residues in contact with LYS 70 (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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30A LEU* 4.0 11.0 - - + -
31A ASN* 2.6 35.2 + - - +
34A THR* 3.4 27.6 + - + +
66A LEU 3.2 15.3 - - - +
67A LEU* 3.2 3.9 + - - +
69A HIS* 1.3 84.5 - - - +
71A ILE* 1.3 62.7 + - - +
73A SER* 3.0 24.5 + - - -
78A GLU* 3.6 26.6 + - + +
79A ALA* 3.4 10.7 + - - -
82A ALA* 3.7 19.7 - - + -
69B HIS* 4.5 1.3 - - - -
75B GLN* 3.8 15.1 - - - +
78B GLU* 4.9 13.2 + - - -
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Residues in contact with ILE 71 (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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67A LEU* 2.9 27.8 + - + +
68A ALA* 3.7 9.0 - - - +
70A LYS* 1.3 75.8 - - - +
72A GLN* 1.3 61.2 + - + +
73A SER 3.2 1.5 + - - +
79A ALA* 3.5 18.7 - - - +
82A ALA* 3.7 19.7 - - + +
83A LEU* 3.7 37.9 - - + +
86A LEU* 3.8 28.0 - - + -
106A PHE* 5.3 1.6 - - + -
110A LEU* 3.8 20.4 - - + -
113A VAL* 3.9 21.5 - - + +
123A ALA* 5.4 0.9 - - - +
127A VAL* 4.3 3.9 - - + +
131A VAL* 4.6 3.4 - - + -
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Residues in contact with GLN 72 (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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68A ALA 3.2 15.0 + - - +
69A HIS* 3.2 8.9 + - - +
70A LYS 3.1 0.8 - - - -
71A ILE* 1.3 78.7 - - + +
73A SER* 1.3 53.6 + - - +
109A GLU* 2.7 54.8 + - - +
112A LYS* 4.4 11.2 - - + +
113A VAL* 4.3 15.3 - - + -
122A TRP* 2.7 35.4 + - + +
123A ALA* 6.1 1.3 - - - -
69B HIS* 3.9 6.4 - - + -
72B GLN* 5.8 0.2 - - - +
122B TRP* 3.5 22.7 - - - -
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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