Contacts of the helix formed by residues 70 - 83 (chain D) in PDB entry 1DVM
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 GLY 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D PRO* 3.7 22.8 - - - +
68D ASP 3.3 0.6 + - - -
69D LYS* 1.3 78.6 - - - +
71D MET* 1.3 58.4 + - - +
73D PRO* 3.6 22.1 - - - +
74D ALA* 3.0 29.8 + - - +
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Residues in contact with MET 71 (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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4D PRO* 3.6 26.2 - - + -
7D TYR* 4.7 10.5 - - + -
8D VAL* 3.3 26.2 - - + +
64D PHE* 3.9 26.2 - - + -
65D LYS 2.9 28.0 - - - +
66D ILE* 3.8 9.4 - - - +
68D ASP* 3.0 30.3 + - + +
69D LYS 3.7 9.0 - - - +
70D GLY* 1.3 79.6 - - - +
72D ALA* 1.3 63.6 + - - +
74D ALA* 3.5 2.1 - - - +
75D LEU* 3.2 29.0 + - - +
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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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66D ILE* 4.0 26.5 + - + +
68D ASP 4.5 0.8 + - - -
71D MET* 1.3 73.1 - - - +
73D PRO* 1.3 64.7 - - + +
74D ALA 3.1 2.2 - - - -
75D LEU* 3.1 4.1 + - - +
76D ARG* 2.7 40.2 + - - +
116D LEU* 3.4 40.5 - - + +
117D PHE* 5.2 1.9 - - + -
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Residues in contact with PRO 73 (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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68D ASP 5.5 0.4 - - - +
70D GLY* 3.6 27.1 - - - +
71D MET 3.7 0.4 - - - +
72D ALA* 1.3 94.2 - - + +
74D ALA* 1.3 55.9 + - - +
76D ARG* 3.1 33.9 + - - +
77D HIS* 2.8 27.7 + - - +
116D LEU* 6.3 0.4 - - + -
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Residues in contact with ALA 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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4D PRO 3.0 30.1 - - - +
5D PRO* 4.5 9.3 - - + +
8D VAL* 4.0 7.4 - - + -
70D GLY 3.0 15.3 + - - +
71D MET 3.4 3.8 + - - +
72D ALA 3.1 0.2 - - - -
73D PRO* 1.3 78.0 - - - +
75D LEU* 1.3 55.4 + - - +
77D HIS* 3.2 8.9 + - - +
78D LEU* 2.7 33.4 + - - +
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Residues in contact with LEU 75 (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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8D VAL* 3.5 32.5 - - + +
12D ALA* 4.8 10.3 - - + -
37D TYR* 4.9 9.4 + - + -
41D SER* 5.8 4.7 - - - +
44D ALA* 4.2 15.3 - - + -
64D PHE* 4.3 11.9 - - + -
66D ILE* 3.8 28.5 - - + -
71D MET 3.2 12.3 + - - +
72D ALA* 3.1 5.1 + - - +
74D ALA* 1.3 75.7 - - - +
76D ARG* 1.3 65.4 + - - +
78D LEU* 3.2 16.3 + - + +
79D TYR* 3.0 23.0 + - - +
117D PHE* 4.6 11.4 - - + -
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Residues in contact with ARG 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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72D ALA* 2.7 14.3 + - - +
73D PRO* 3.1 42.1 - - - +
75D LEU* 1.3 77.1 - - - +
77D HIS* 1.3 60.0 + - - +
79D TYR* 3.3 15.4 + - - +
80D LYS* 3.4 27.6 + - - +
115D ARG 3.1 6.5 + - - -
116D LEU* 2.9 47.4 + - - +
117D PHE* 4.6 10.3 - - - +
118D ARG* 3.4 49.9 - - + +
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Residues in contact with HIS 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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73D PRO 2.8 19.1 + - - +
74D ALA* 3.3 10.1 + - - +
75D LEU 3.1 0.2 - - - -
76D ARG* 1.3 76.7 - - - +
78D LEU* 1.3 64.3 + - - +
80D LYS* 3.5 16.0 + - + +
81D GLU* 3.1 47.7 + - + +
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Residues in contact with LEU 78 (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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5D PRO 5.5 2.0 - - - +
8D VAL* 5.9 0.7 - - + -
9D ALA* 3.8 21.8 - - + -
12D ALA* 5.9 0.7 - - + -
37D TYR* 4.2 18.2 - - + -
74D ALA 2.7 18.6 + - - +
75D LEU* 3.2 17.7 + - + +
77D HIS* 1.3 73.6 - - - +
79D TYR* 1.3 64.5 + - - +
81D GLU* 4.3 4.3 - - - +
82D LEU* 3.2 47.9 + - + +
364D HIS* 4.3 5.4 - - + +
367D THR* 3.5 36.8 - - + +
369D THR* 3.3 21.3 - - + +
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Residues in contact with TYR 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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37D TYR* 3.6 22.0 + + - +
75D LEU 3.0 11.5 + - - +
76D ARG* 3.6 10.3 - - - +
77D HIS 3.2 0.2 - - - -
78D LEU* 1.3 75.6 - - - +
80D LYS* 1.3 70.5 + - + +
82D LEU* 2.9 7.4 + - + +
83D MET* 2.8 55.0 + - + +
93D THR* 3.7 35.6 + - - -
94D THR* 5.5 0.5 - - - -
95D ASP* 5.1 10.1 - - - -
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Residues in contact with LYS 80 (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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76D ARG* 3.4 25.6 - - - +
77D HIS* 3.7 17.0 - - + +
79D TYR* 1.3 79.6 - - + +
81D GLU* 1.3 57.1 + - - +
83D MET* 3.3 6.2 + - - +
84D GLY* 2.9 27.9 + - - -
118D ARG* 5.9 8.9 - - - +
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Residues in contact with GLU 81 (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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77D HIS* 3.1 42.8 + - + +
78D LEU* 3.8 6.6 - - + +
80D LYS* 1.3 79.1 - - - +
82D LEU* 1.3 51.2 + - - +
84D GLY* 3.3 4.3 + - - -
86D TRP* 2.7 34.9 + - + -
364D HIS* 3.2 30.6 - - + +
366D PRO* 3.7 12.5 - - - +
367D THR* 3.5 20.4 - - - +
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Residues in contact with LEU 82 (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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37D TYR* 3.7 36.8 - - + +
78D LEU* 3.2 32.5 + - + +
79D TYR* 2.9 5.9 + - + +
81D GLU* 1.3 80.0 - - - +
83D MET* 1.3 63.5 + - + +
84D GLY 3.3 0.9 - - - -
86D TRP* 3.3 19.9 + - + +
87D ASN* 2.5 30.7 + - - -
91D ILE* 4.5 5.6 - - + +
364D HIS* 3.8 27.4 - - + -
369D THR* 5.4 0.2 - - + -
371D LEU* 3.7 33.9 - - + -
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Residues in contact with MET 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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37D TYR* 6.3 0.9 - - + -
79D TYR* 2.8 59.3 + - + +
80D LYS* 3.5 6.1 - - - +
82D LEU* 1.3 92.0 - - + +
84D GLY* 1.3 67.4 + - - +
87D ASN* 3.6 16.1 - - - +
91D ILE* 3.6 41.7 - - + +
92D SER* 5.1 1.1 - - - -
93D THR* 4.4 11.9 - - + +
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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