Contacts of the helix formed by residues 71 - 88 (chain A) in PDB entry 3DH1
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 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASN* 3.5 21.8 + - - +
62A VAL* 4.2 4.4 - - + +
68A ALA 3.8 22.4 + - - -
69A THR* 2.8 12.9 + - - +
70A ARG* 1.3 76.0 - - - +
72A ALA* 1.3 57.2 - - - +
73A GLU* 3.5 10.5 - - - +
74A MET* 2.7 25.2 + - + -
75A VAL* 3.2 9.3 + - - +
107A CYS* 3.5 14.5 - - + -
109A MET* 5.3 2.4 - - - -
110A CYS* 3.7 10.7 - - - -
131A PHE* 5.5 1.1 - + - -
201A ZN 2.0 36.0 - - - -
116D LEU* 4.1 18.4 - - + +
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Residues in contact with ALA 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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44A VAL* 3.6 32.5 - - + +
46A CYS* 3.6 9.0 - - - +
58A GLY* 3.4 21.3 - - - +
59A ARG 3.5 22.7 - - - -
60A ASN* 3.0 10.9 + - - +
71A HIS* 1.3 71.6 - - - +
73A GLU* 1.3 62.5 + - - +
75A VAL* 3.4 4.3 + - - +
76A ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 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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44A VAL* 4.1 13.7 - - - +
46A CYS* 3.9 9.2 - - - -
48A MET* 5.1 0.5 - - - +
60A ASN* 4.5 0.5 - - - +
71A HIS* 3.5 7.6 + - - +
72A ALA* 1.3 93.6 + - - +
74A MET* 1.3 57.5 + - + +
76A ALA* 3.4 2.6 + - - +
77A ILE* 3.0 38.3 + - + +
100A LEU* 4.4 13.5 - - + -
102A VAL* 4.3 22.0 - - + -
104A VAL 4.7 3.1 - - - +
105A GLU 4.8 0.2 - - - +
106A PRO* 3.4 30.5 - - + +
110A CYS* 3.5 28.9 - - + -
114A LEU* 5.3 5.4 - - + -
201A ZN 3.6 4.7 - - - -
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Residues in contact with MET 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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69A THR* 3.5 23.6 - - - +
70A ARG* 4.6 6.7 - - + -
71A HIS 2.7 15.8 + - - +
73A GLU* 1.3 69.5 - - - +
75A VAL* 1.3 62.1 + - - +
77A ILE* 3.5 13.3 + - + +
78A ASP* 3.2 28.2 + - - +
109A MET* 3.4 28.0 - - + -
110A CYS* 4.4 13.0 - - - -
113A ALA* 4.3 21.8 - - - -
69D THR* 4.4 12.3 - - + +
74D MET* 4.1 20.9 - - + -
109D MET* 4.2 8.3 - - + -
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Residues in contact with VAL 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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57A LYS 3.7 4.5 - - - +
58A GLY* 3.6 19.7 - - - -
59A ARG 3.4 19.7 - - - +
61A GLU* 3.8 31.6 - - + +
70A ARG* 4.4 17.2 - - + +
71A HIS 3.2 9.6 + - - +
72A ALA 3.5 8.1 - - - +
74A MET* 1.3 75.8 - - - +
76A ALA* 1.3 61.6 + - - +
78A ASP* 3.3 9.6 + - - +
79A GLN* 3.1 28.7 + - + +
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Residues in contact with ALA 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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46A CYS* 3.7 19.5 - - - -
48A MET* 3.9 15.5 - - + -
56A GLY* 4.1 6.0 - - - +
57A LYS 3.3 21.3 + - - +
72A ALA 3.1 13.9 + - - +
73A GLU* 3.5 9.0 - - - +
75A VAL* 1.3 74.6 - - - +
77A ILE* 1.3 60.4 + - - +
79A GLN* 3.0 5.2 + - - +
80A VAL* 2.9 33.5 + - - +
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Residues in contact with ILE 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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48A MET* 4.5 8.7 - - + -
73A GLU* 3.0 26.1 + - + +
74A MET* 3.8 22.2 - - + +
75A VAL 3.4 0.2 - - - -
76A ALA* 1.3 74.1 - - - +
78A ASP* 1.3 61.3 + - - +
80A VAL* 3.3 1.9 + - - +
81A LEU* 2.9 37.6 + - + +
95A PHE* 4.0 16.8 - - + -
113A ALA* 4.6 7.6 - - + -
114A LEU* 4.2 23.8 - - + -
117A MET* 3.6 39.0 - - + -
67D ASN* 4.9 3.8 - - - +
69D THR* 4.8 6.1 - - + +
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Residues in contact with ASP 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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70A ARG* 5.9 2.3 - - - -
74A MET* 3.2 15.0 + - - +
75A VAL* 3.5 11.5 - - - +
76A ALA 3.3 0.2 - - - -
77A ILE* 1.3 79.8 - - - +
79A GLN* 1.3 59.1 + - + +
81A LEU* 3.5 16.6 + - - +
82A ASP* 3.0 25.8 + - - +
85A ARG* 6.2 0.2 - - - -
67D ASN* 4.5 6.6 + - - -
70D ARG* 4.9 5.2 + - - -
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Residues in contact with GLN 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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55A VAL 3.7 3.2 - - - +
56A GLY* 3.7 8.7 - - - -
57A LYS* 2.9 39.1 + - - +
75A VAL* 3.1 20.2 + - + +
76A ALA 3.0 10.1 + - - +
78A ASP* 1.3 74.8 - - + +
80A VAL* 1.3 61.0 + - - +
82A ASP* 3.1 10.4 + - + +
83A TRP* 2.8 27.4 + - - +
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Residues in contact with VAL 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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48A MET* 3.7 24.0 - - + -
55A VAL* 3.3 46.0 - - + +
56A GLY* 3.8 2.2 - - - -
76A ALA 2.9 22.1 + - - +
77A ILE 3.7 1.3 - - - +
79A GLN* 1.3 69.2 - - - +
81A LEU* 1.3 66.3 + - - +
83A TRP* 2.9 12.9 + - - +
84A CYS* 2.9 13.6 + - - +
94A VAL* 4.1 17.9 - - + -
95A PHE* 3.4 32.3 - - + -
98A THR* 5.1 1.1 - - - +
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Residues in contact with LEU 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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77A ILE* 2.9 34.5 + - + +
78A ASP* 3.6 13.2 - - - +
80A VAL* 1.3 75.9 - - - +
82A ASP* 1.3 59.4 + - - +
84A CYS* 3.4 7.8 - - - +
85A ARG* 3.2 31.4 + - - +
91A PRO* 4.3 13.9 - - + -
95A PHE* 4.1 13.5 - - + -
117A MET* 4.4 1.3 - - + -
65D THR 4.8 4.3 - - - +
66D LYS 3.9 13.2 - - - +
67D ASN* 3.1 49.8 - - + +
70D ARG* 4.3 8.7 - - - +
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Residues in contact with ASP 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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78A ASP 3.0 15.6 + - - +
79A GLN* 3.1 13.4 + - + +
81A LEU* 1.3 73.5 - - - +
83A TRP* 1.3 64.4 + - - +
85A ARG* 3.0 42.6 + - - +
86A GLN* 3.0 46.8 + - - +
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Residues in contact with TRP 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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50A TYR* 4.2 20.6 - + - -
53A GLU* 3.4 41.2 + - + +
54A VAL 5.0 2.0 - - - -
55A VAL* 3.1 42.3 - - + +
79A GLN 2.8 12.7 + - - +
80A VAL 2.9 8.0 + - - +
82A ASP* 1.3 72.3 - - - +
84A CYS* 1.3 74.8 + - - +
86A GLN* 3.3 11.6 + - + +
87A SER* 3.0 49.1 + - - -
89A LYS* 4.4 8.3 - - + -
94A VAL* 4.2 17.7 - - + -
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Residues in contact with CYS 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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80A VAL* 2.9 19.4 + - - -
81A LEU* 3.4 12.6 - - - +
83A TRP* 1.3 75.8 - - - +
85A ARG* 1.3 68.2 + - - +
86A GLN 3.0 0.9 + - - -
87A SER* 3.9 5.6 - - - -
88A GLY* 3.1 20.3 + - - -
89A LYS 3.4 17.4 - - - +
91A PRO* 3.7 31.6 - - + -
94A VAL* 3.6 36.3 - - - -
95A PHE* 5.1 0.7 - - - -
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Residues in contact with ARG 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 LEU* 3.2 18.9 + - - +
82A ASP* 3.0 36.9 + - - +
84A CYS* 1.3 79.5 - - - +
86A GLN* 1.3 64.0 + - + +
88A GLY* 3.9 6.9 + - - -
70D ARG* 4.3 21.4 - - - +
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Residues in contact with GLN 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 ASP* 3.0 35.4 + - - +
83A TRP* 3.3 11.7 + - + +
84A CYS 3.1 0.8 - - - -
85A ARG* 1.3 81.2 - - + +
87A SER* 1.3 61.1 + - - +
88A GLY 3.4 0.7 - - - -
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Residues in contact with SER 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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83A TRP* 3.0 45.3 + - - -
84A CYS 3.5 1.4 + - - -
86A GLN* 1.3 77.6 - - - +
88A GLY* 1.3 56.9 + - - +
89A LYS* 3.1 36.4 + - - +
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Residues in contact with GLY 88 (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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84A CYS 3.1 7.4 + - - -
85A ARG 3.9 5.3 + - - -
86A GLN 3.4 3.0 - - - -
87A SER* 1.3 76.3 - - - +
89A LYS* 1.3 63.6 + - - +
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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