Contacts of the helix formed by residues 64 - 79 (chain D) in PDB entry 3RMD
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 ASN 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D ASP* 3.1 40.0 - - + +
32D GLU* 5.7 3.4 - - + +
33D TYR 3.9 10.8 - - - +
35D PRO* 3.9 6.3 - - - -
62D PHE* 3.3 4.2 - - - +
63D ALA* 1.3 92.0 + - - +
65D MET* 1.3 66.8 + - - +
66D ARG* 3.5 2.8 - - - +
67D ASP* 3.1 46.4 + - - +
68D ALA 3.3 8.1 + - - -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLN* 3.3 33.9 - - - +
12D GLY 4.4 5.8 - - - +
13D ASP* 3.4 37.2 + - - +
14D SER 3.9 3.6 - - - +
15D ILE* 3.2 28.3 - - + +
33D TYR* 3.5 21.9 + - + +
35D PRO* 3.8 21.8 - - + +
64D ASN* 1.3 73.5 - - - +
66D ARG* 1.3 62.8 + - - +
68D ALA* 3.2 2.6 + - - +
69D SER* 2.8 27.9 + - - +
88D PHE* 3.8 29.3 - - + -
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Residues in contact with ARG 66 (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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12D GLY 5.4 1.1 + - - -
13D ASP* 2.7 30.1 + - - +
64D ASN* 3.1 5.8 + - - +
65D MET* 1.3 73.4 - - - +
67D ASP* 1.3 60.9 + - - +
69D SER* 3.3 7.1 + - - -
70D GLN* 2.9 37.4 + - + +
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Residues in contact with ASP 67 (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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62D PHE* 3.7 16.5 - - + -
63D ALA* 3.5 14.6 + - - +
64D ASN* 3.1 35.7 + - - +
66D ARG* 1.3 77.0 - - - +
68D ALA* 1.3 55.4 + - - +
70D GLN* 3.2 8.4 + - - +
71D TRP* 2.7 36.4 + - - +
74D ARG* 4.9 1.8 + - - +
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Residues in contact with ALA 68 (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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35D PRO* 3.6 22.2 - - + -
37D LEU* 3.9 11.2 - - + +
62D PHE* 3.5 19.9 - - + -
64D ASN 3.3 1.8 + - - -
65D MET 3.2 9.4 + - - +
67D ASP* 1.3 77.3 - - - +
69D SER* 1.3 64.0 + - - +
71D TRP* 3.1 5.0 - - - +
72D ILE* 3.0 27.5 + - - +
88D PHE* 3.4 21.1 - - + -
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Residues in contact with SER 69 (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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65D MET* 2.8 15.0 + - - +
66D ARG* 3.4 10.1 - - - -
68D ALA* 1.3 75.6 - - - +
70D GLN* 1.3 70.6 + - - +
72D ILE* 2.9 21.9 + - - +
73D LYS* 3.0 11.8 + - - +
88D PHE* 3.4 18.9 - - - -
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Residues in contact with GLN 70 (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 ARG* 2.9 25.9 + - + +
67D ASP* 3.5 8.7 - - - +
69D SER* 1.3 78.6 - - - +
71D TRP* 1.3 63.6 + - - +
73D LYS* 3.0 12.9 + - - +
74D ARG* 3.0 34.9 + - - +
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Residues in contact with TRP 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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37D LEU* 3.4 33.7 - - + -
38D PHE* 3.7 24.5 - - - -
39D ALA* 4.2 12.1 - - + -
60D LYS* 5.2 10.0 - - + +
62D PHE* 3.2 38.8 - + + -
67D ASP 2.7 10.6 + - - +
68D ALA 3.1 9.4 - - - +
70D GLN* 1.3 73.5 - - - +
72D ILE* 1.3 65.8 + - + +
74D ARG* 3.3 31.9 + - - +
75D MET* 2.9 69.6 + - + +
82D ALA* 3.8 21.3 - - + -
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Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LEU* 3.8 26.7 - - + -
68D ALA 3.0 13.2 + - - +
69D SER* 2.9 14.1 + - - +
71D TRP* 1.3 79.5 - - + +
73D LYS* 1.3 67.0 + - - +
75D MET* 3.7 4.0 - - - +
76D GLU* 2.8 59.5 + - + +
82D ALA* 4.3 12.3 - - + +
86D ASP* 4.0 29.2 - - + +
88D PHE* 5.1 3.8 - - + -
382D GLN* 5.7 0.4 - - + -
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Residues in contact with LYS 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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69D SER 3.0 11.1 + - - +
70D GLN* 3.0 17.0 + - - +
72D ILE* 1.3 78.7 - - - +
74D ARG* 1.3 62.9 + - - +
76D GLU* 3.7 6.3 - - - +
77D ASP* 2.9 33.5 + - - +
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Residues in contact with ARG 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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67D ASP* 4.9 1.6 + - - +
70D GLN* 3.0 19.2 + - - +
71D TRP* 3.3 42.6 - - - +
73D LYS* 1.3 75.3 - - - +
75D MET* 1.3 58.1 + - + +
77D ASP* 2.8 30.5 + - + +
78D ILE* 3.0 32.6 + - + +
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Residues in contact with MET 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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39D ALA* 4.6 8.7 - - + -
71D TRP* 2.9 66.7 + - + +
72D ILE 3.7 3.8 - - - +
74D ARG* 1.3 77.8 - - + +
76D GLU* 1.3 58.5 + - - +
78D ILE* 3.4 11.2 + - - +
79D GLY 2.9 9.4 + - - -
80D LEU* 2.8 69.9 + - + +
81D GLU 3.5 20.2 - - - +
82D ALA* 4.1 7.9 - - + -
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Residues in contact with GLU 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 ILE* 2.8 40.2 + - + +
73D LYS* 3.8 6.0 - - - +
75D MET* 1.3 74.9 - - + +
77D ASP* 1.3 67.7 + - - +
79D GLY* 3.3 10.4 + - - +
80D LEU 4.1 3.8 - - - +
382D GLN* 2.7 46.1 + - - +
383D GLY 4.6 2.6 - - - +
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Residues in contact with ASP 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 LYS* 2.9 23.1 + - - +
74D ARG* 2.8 13.5 + - - +
76D GLU* 1.3 81.1 - - - +
78D ILE* 1.3 63.7 + - + +
79D GLY* 3.2 1.6 + - - -
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Residues in contact with ILE 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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74D ARG* 3.0 33.6 + - + +
75D MET* 3.6 12.8 - - - +
77D ASP* 1.3 76.1 - - + +
79D GLY* 1.3 58.5 + - - +
80D LEU* 4.5 24.2 - - + +
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Residues in contact with GLY 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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75D MET 2.9 3.6 + - - -
76D GLU* 3.3 10.3 + - - -
77D ASP 3.1 5.1 - - - -
78D ILE* 1.3 79.6 - - - +
80D LEU* 1.3 66.0 + - - +
81D GLU 4.1 0.9 + - - -
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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