Contacts of the helix formed by residues 70 - 83 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PRO* 4.4 3.8 - - - -
68B ASP 3.5 1.2 + - - -
69B LYS* 1.3 71.5 - - - +
71B MET* 1.3 64.4 + - - +
73B PRO* 3.4 24.6 - - - +
74B ALA* 3.0 29.8 + - - +
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PRO* 4.0 15.3 - - + -
7B TYR* 3.8 37.0 - - + -
8B VAL* 3.9 21.9 - - + +
11B LEU* 4.6 0.7 - - - -
64B PHE* 3.9 30.7 - - + -
65B LYS 3.7 22.0 - - - +
66B ILE* 3.9 4.3 - - - +
68B ASP* 3.6 21.9 + - + +
69B LYS 3.2 7.0 - - - +
70B GLY* 1.3 75.9 - - - +
72B ALA* 1.3 66.0 + - - +
74B ALA* 3.3 5.2 + - - +
75B LEU* 3.1 27.3 + - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 3.7 30.8 + - + +
71B MET* 1.3 76.1 - - - +
73B PRO* 1.4 66.5 - - + +
75B LEU* 2.9 7.2 + - - +
76B ARG* 2.9 30.1 + - - +
116B LEU* 3.5 45.3 - - + +
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Residues in contact with PRO 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASP 5.3 0.9 - - - +
70B GLY* 3.4 28.5 - - - +
71B MET 3.7 0.2 - - - +
72B ALA* 1.4 95.9 - - + +
74B ALA* 1.3 55.1 + - - +
76B ARG* 3.4 34.4 + - - +
77B HIS* 3.0 27.5 + - - +
116B LEU* 6.0 1.1 - - + -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PRO* 3.9 18.2 - - + -
5B PRO* 4.0 8.6 - - + +
8B VAL* 3.4 24.9 - - + -
70B GLY 3.0 22.2 + - - +
71B MET 3.3 6.3 - - - +
72B ALA 3.1 0.2 - - - -
73B PRO* 1.3 78.0 - - - +
75B LEU* 1.3 52.7 + - - +
77B HIS* 3.4 6.4 + - - +
78B LEU* 2.7 35.3 + - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.6 27.4 - - + -
12B ALA* 5.2 8.3 - - + -
37B TYR* 4.8 7.5 + - + -
41B SER* 6.2 4.5 - - - -
44B ALA* 4.6 8.5 - - + -
64B PHE* 4.2 11.9 - - + -
66B ILE* 3.5 31.4 - - + -
71B MET 3.1 10.7 + - - +
72B ALA* 2.9 7.9 + - - +
74B ALA* 1.3 75.9 - - - +
76B ARG* 1.3 60.0 + - - +
77B HIS 3.3 0.2 - - - -
78B LEU* 3.8 20.0 - - + +
79B TYR* 2.9 29.6 + - - +
117B PHE* 5.1 8.1 - - + -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 2.9 6.4 + - - +
73B PRO* 3.6 49.0 - - - +
74B ALA 3.3 0.2 - - - -
75B LEU* 1.3 75.2 - - - +
77B HIS* 1.3 59.3 + - - +
79B TYR* 3.5 6.6 + - + +
80B LYS* 3.1 39.9 + - + +
115B ARG* 3.6 10.5 + - - +
116B LEU* 3.3 40.7 + - - +
117B PHE* 4.4 4.5 - - - +
118B ARG* 3.9 42.0 - - + +
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 3.1 34.7 - - + +
73B PRO 3.0 17.3 + - - +
74B ALA* 3.6 6.5 - - - +
76B ARG* 1.3 75.1 - - - +
78B LEU* 1.3 57.5 - - - +
80B LYS* 3.2 8.0 + - - +
81B GLU* 2.9 56.0 + - + +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 4.2 13.5 - - + +
8B VAL* 4.8 1.6 - - + -
9B ALA* 4.1 23.8 - - + +
12B ALA* 5.4 1.8 - - + -
37B TYR* 4.2 15.3 - - + -
74B ALA 2.7 21.3 + - - +
75B LEU* 3.8 26.9 - - + +
76B ARG 3.4 0.2 - - - -
77B HIS* 1.3 78.0 - - - +
79B TYR* 1.3 59.5 + - - +
81B GLU* 3.3 5.4 + - - +
82B LEU* 3.2 42.6 + - + +
364B HIS* 5.0 0.2 - - - +
367B THR* 4.0 21.1 - - + +
369B THR* 3.4 23.1 - - - +
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 3.4 25.3 + + - +
75B LEU 2.9 19.1 + - - +
76B ARG* 3.7 6.1 - - + +
78B LEU* 1.3 76.2 - - - +
80B LYS* 1.3 74.5 + - + +
82B LEU* 3.2 3.7 + - - +
83B MET* 2.8 67.6 + - + +
93B THR* 3.7 28.4 + - - -
95B ASP* 5.4 6.3 - - - -
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Residues in contact with LYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.1 26.0 + - + +
77B HIS* 3.2 7.2 + - - +
79B TYR* 1.3 89.0 - - + +
81B GLU* 1.3 60.3 + - - +
82B LEU 3.3 0.2 - - - -
83B MET 3.3 20.7 - - - +
84B GLY* 5.3 0.3 - - - -
86B TRP* 5.4 1.2 + - - -
118B ARG* 5.9 7.5 - - - +
85C PRO* 5.1 13.6 - - + +
88C LYS* 5.2 12.8 - - - +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 5.3 1.4 - - - +
77B HIS* 2.9 47.0 + - + +
78B LEU* 3.7 8.3 - - + +
79B TYR 3.2 0.2 - - - -
80B LYS* 1.3 77.8 - - - +
82B LEU* 1.3 59.8 + - - +
86B TRP* 3.3 17.1 + - - -
364B HIS* 3.4 22.4 + - + +
366B PRO* 4.5 5.6 - - - +
367B THR* 3.0 32.7 - - - +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 4.0 21.3 - - + -
78B LEU* 3.2 34.1 + - + +
79B TYR* 3.2 4.2 + - - +
81B GLU* 1.3 80.9 - - - +
83B MET* 1.3 76.1 + - + +
84B GLY 3.9 0.2 + - - -
86B TRP* 2.8 31.3 + - + +
87B ASN* 4.4 0.2 - - - +
91B ILE* 4.1 5.5 - - - +
233B LEU* 5.1 0.2 - - + -
364B HIS* 3.4 41.5 - - + +
369B THR* 4.4 3.4 - - + -
371B LEU* 3.7 35.2 - - + -
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Residues in contact with MET 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 5.0 6.7 - - + -
79B TYR* 2.8 56.7 + - + +
80B LYS* 3.3 20.2 - - - +
82B LEU* 1.3 97.1 - - + +
84B GLY* 1.3 58.3 + - - +
86B TRP* 4.3 1.6 - - - -
87B ASN* 5.7 0.4 - - - +
91B ILE* 3.7 31.6 - - + +
92B SER* 5.1 1.8 - - - -
93B THR* 3.4 39.7 - - + +
371B LEU* 5.9 2.9 - - + -
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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