Contacts of the helix formed by residues 71 - 88 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.0 20.8 - - + +
59D ARG 4.3 0.9 - - - -
60D ASN* 3.5 17.1 + - - +
62D VAL* 4.0 10.8 - - + +
68D ALA 3.3 24.5 + - - -
69D THR 2.8 12.9 + - - +
70D ARG* 1.3 75.1 - - - +
72D ALA* 1.3 70.1 + - - +
73D GLU* 3.6 6.5 - - - +
74D MET* 2.8 14.2 + - + +
75D VAL* 3.2 9.0 + - - +
107D CYS* 3.7 13.4 - - + -
109D MET* 5.3 2.0 - - - -
110D CYS* 3.8 9.3 - - - -
131D PHE* 5.7 0.9 - + - -
201D ZN 2.2 37.9 - - - -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D VAL* 3.4 47.1 - - + +
45D GLY* 4.3 0.7 - - - -
46D CYS* 3.5 15.9 - - + -
58D GLY* 3.5 15.3 - - - +
59D ARG 3.6 14.6 - - - -
60D ASN* 2.9 11.7 + - - +
71D HIS* 1.3 71.1 - - - +
73D GLU* 1.3 62.5 + - - +
75D VAL* 3.4 3.6 + - - +
76D ALA 3.2 17.2 + - - -
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D VAL* 4.1 8.8 - - - +
46D CYS* 4.0 7.2 - - - -
48D MET* 5.0 0.5 - - - +
60D ASN* 4.6 0.2 - - - +
71D HIS* 2.8 5.9 + - - +
72D ALA* 1.3 90.4 + - - +
74D MET* 1.3 63.1 + - - +
76D ALA* 3.3 5.4 - - - +
77D ILE* 3.1 28.1 + - + +
100D LEU* 4.3 13.0 - - + -
102D VAL* 4.0 26.0 - - + -
104D VAL 4.9 1.9 - - - +
105D GLU 4.9 0.3 - - - +
106D PRO* 3.4 19.5 - - + +
110D CYS* 3.3 38.2 - - + +
114D LEU* 5.0 10.3 - - + +
201D ZN 3.3 8.9 - - - -
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Residues in contact with MET 74 (chain D).
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* 4.5 19.3 - - + +
74A MET* 4.1 25.4 - - + -
109A MET* 5.0 0.7 - - + -
69D THR* 3.2 25.6 - - - +
70D ARG* 4.5 6.5 - - + -
71D HIS 2.8 14.3 + - - +
73D GLU* 1.3 71.8 - - - +
75D VAL* 1.3 65.7 + - - +
77D ILE* 3.3 16.7 + - + +
78D ASP* 3.3 28.7 + - - +
109D MET* 3.8 15.9 - - + -
110D CYS* 4.4 14.4 - - - -
113D ALA* 4.3 22.0 - - - -
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Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LYS 4.0 2.7 - - - +
58D GLY* 3.8 17.3 - - - -
59D ARG 3.5 21.5 - - - +
61D GLU* 3.6 30.5 - - - +
70D ARG* 4.2 20.0 - - + +
71D HIS 3.2 7.8 + - - +
72D ALA 3.6 8.1 - - - +
74D MET* 1.3 75.7 - - - +
76D ALA* 1.3 63.4 + - - +
78D ASP* 3.4 8.9 + - - +
79D GLN* 3.3 26.3 + - + +
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D CYS* 3.6 28.0 - - - -
48D MET* 3.6 20.0 - - + -
56D GLY* 4.2 2.6 - - - -
57D LYS 3.5 18.8 + - - +
72D ALA 3.2 4.2 + - - -
73D GLU* 3.3 11.2 - - - +
75D VAL* 1.3 75.2 - - - +
77D ILE* 1.3 66.6 + - - +
79D GLN* 2.9 15.0 + - - +
80D VAL* 2.9 18.2 + - - +
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASN* 4.8 4.5 - - - +
69A THR* 4.9 5.6 - - + +
48D MET* 4.5 10.1 - - + -
73D GLU* 3.1 18.7 + - + +
74D MET* 3.3 26.2 + - + +
76D ALA* 1.3 75.7 - - - +
78D ASP* 1.3 60.6 + - - +
80D VAL* 3.4 3.1 + - - +
81D LEU* 3.0 36.4 + - + +
95D PHE* 3.8 17.6 - - + -
113D ALA* 4.7 7.4 - - + -
114D LEU* 4.2 22.4 - - + -
117D MET* 3.6 40.2 - - + -
119D ILE* 5.6 0.2 - - + -
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Residues in contact with ASP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 4.5 6.2 + - - -
70A ARG* 5.0 4.4 + - - -
74D MET* 3.3 13.5 + - - +
75D VAL* 3.6 11.4 - - - +
76D ALA 3.1 0.8 - - - -
77D ILE* 1.3 83.6 - - - +
79D GLN* 1.3 51.9 + - + +
81D LEU* 3.2 17.1 + - - +
82D ASP* 2.8 35.0 + - - +
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Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D VAL 3.7 4.0 - - - +
56D GLY* 3.7 8.7 - - - -
57D LYS* 2.8 47.7 + - - +
58D GLY* 5.8 0.2 - - - -
75D VAL* 3.3 14.0 + - + +
76D ALA 2.9 8.4 + - - +
78D ASP* 1.3 80.2 - - + +
80D VAL* 1.3 57.3 + - - +
82D ASP* 3.2 10.3 + - + +
83D TRP* 2.7 27.0 + - - +
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Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D MET* 3.7 26.2 - - + -
55D VAL* 3.4 42.0 - - + +
56D GLY* 3.8 4.3 - - - -
76D ALA 2.9 14.2 + - - +
77D ILE 3.8 0.9 - - - +
79D GLN* 1.3 73.6 - - - +
81D LEU* 1.3 59.2 + - - +
83D TRP* 3.1 3.0 + - - +
84D CYS* 2.9 28.8 + - - -
94D VAL* 3.9 21.1 - - + -
95D PHE* 3.6 28.0 - - + -
98D THR* 5.3 0.9 - - - +
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR 4.9 4.0 - - - +
66A LYS 4.2 3.8 - - - +
67A ASN* 3.4 47.6 - - + +
70A ARG* 4.3 9.6 - - - +
77D ILE* 3.0 32.3 + - + +
78D ASP* 3.2 14.6 + - - +
80D VAL* 1.3 76.9 - - - +
82D ASP* 1.3 62.5 + - - +
84D CYS* 3.4 6.8 + - - +
85D ARG* 3.1 22.0 + - - +
91D PRO* 4.1 24.2 - - + -
95D PHE* 4.1 13.2 - - + -
117D MET* 4.4 0.4 - - + -
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Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ASP 2.8 14.4 + - - +
79D GLN* 3.3 14.4 - - + +
81D LEU* 1.3 75.6 - - - +
83D TRP* 1.3 65.1 + - - +
85D ARG* 3.2 33.2 + - - +
86D GLN* 2.8 43.0 + - - +
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Residues in contact with TRP 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D TYR* 4.2 21.8 - + - -
53D GLU* 3.3 41.4 + - + +
54D VAL 4.9 1.8 + - - -
55D VAL* 2.9 42.0 - - + +
79D GLN 2.7 17.3 + - - +
80D VAL 3.2 9.4 - - - +
82D ASP* 1.3 74.9 - - - +
84D CYS* 1.3 65.6 + - - +
86D GLN* 3.2 9.5 + - + +
87D SER* 2.9 54.2 + - - -
89D LYS* 4.1 15.0 - - + -
94D VAL* 4.3 11.9 - - + -
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Residues in contact with CYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D VAL* 2.9 21.4 + - - -
81D LEU* 3.6 8.5 - - - +
82D ASP 3.3 0.2 - - - -
83D TRP* 1.3 75.4 - - - +
85D ARG* 1.3 68.5 + - - +
87D SER* 3.7 7.9 - - - -
88D GLY* 3.0 21.5 + - - -
89D LYS 3.2 21.3 + - - +
90D SER 4.1 0.2 - - - -
91D PRO* 3.8 30.7 - - + -
94D VAL* 3.4 38.1 - - - -
95D PHE* 4.9 0.9 - - - -
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Residues in contact with ARG 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU 3.1 10.7 + - - +
82D ASP* 3.2 27.2 + - - +
84D CYS* 1.3 82.5 - - - +
86D GLN* 1.3 68.7 + - + +
88D GLY* 3.8 7.1 + - - -
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ASP* 2.8 36.8 + - - +
83D TRP* 3.2 8.0 + - - +
84D CYS 3.1 0.4 - - - -
85D ARG* 1.3 85.3 - - + +
87D SER* 1.3 60.9 + - - +
88D GLY 3.3 2.8 + - - -
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Residues in contact with SER 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D TRP* 2.9 45.4 + - - -
84D CYS 3.4 1.4 + - - -
86D GLN* 1.3 76.0 - - - +
88D GLY* 1.3 56.5 + - - +
89D LYS* 2.9 40.3 + - - +
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Residues in contact with GLY 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D CYS 3.0 7.5 + - - -
85D ARG 3.8 6.1 + - - -
86D GLN 3.3 4.0 + - - -
87D SER* 1.3 75.4 - - - +
89D LYS* 1.3 63.7 + - - +
90D SER 3.8 0.7 + - - -
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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
------------------------------------------------------------
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