Contacts of the helix formed by residues 64 - 78 (chain D) in PDB entry 4RHW
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 ASP 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 4.0 13.3 - - - +
34D PHE* 4.4 6.0 - - - -
60D ILE* 5.2 0.3 - - - +
63D LYS* 1.3 80.2 - - - +
65D ASN* 1.3 68.3 + - - +
66D ASP* 3.4 14.2 + - - +
67D SER* 2.8 48.3 + - - -
68D TYR* 3.3 6.4 + - - +
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Residues in contact with ASN 65 (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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1D MET* 4.3 6.9 - - - +
2D ASP* 3.0 50.6 + - - +
64D ASP* 1.3 76.8 - - - +
66D ASP* 1.3 68.0 + - - +
68D TYR* 3.1 16.1 + - - +
69D VAL* 3.1 16.7 + - - +
92D PRO* 3.0 28.4 - - + +
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Residues in contact with ASP 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.4 34.3 - - + -
64D ASP* 3.7 9.1 - - - +
65D ASN* 1.3 78.9 - - - +
67D SER* 1.3 53.3 + - - +
69D VAL* 3.0 11.1 + - - +
70D SER* 2.7 35.2 + - - -
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Residues in contact with SER 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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29D MET* 3.8 8.1 - - - +
34D PHE* 3.8 23.6 - - - +
60D ILE* 4.7 4.6 - - - +
63D LYS* 3.3 39.7 + - - +
64D ASP* 2.8 32.3 + - - -
66D ASP* 1.3 77.9 - - - +
68D TYR* 1.3 58.3 + - - +
70D SER* 3.5 2.8 - - - -
71D PHE* 3.1 22.0 + - - +
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Residues in contact with TYR 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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1D MET* 2.3 44.4 - - + -
5D ALA 3.4 11.9 - - - -
8D CYS* 3.7 7.3 - - - -
9D LEU* 3.8 23.8 - - + -
60D ILE* 4.9 4.9 - - + +
64D ASP 3.3 3.4 + - - +
65D ASN* 3.1 13.5 + - - +
67D SER* 1.3 77.5 - - - +
69D VAL* 1.3 62.6 + - - +
71D PHE* 3.2 10.0 + + - +
72D TYR* 2.8 28.2 + - + +
87D LEU* 2.8 49.1 + - + +
90D GLY* 3.7 23.7 - - - -
91D ILE* 4.0 9.9 - - + -
92D PRO* 3.8 15.0 - - + -
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Residues in contact with VAL 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 ASN 3.1 13.6 + - - +
66D ASP* 3.0 13.7 + - - +
68D TYR* 1.3 73.3 - - - +
70D SER* 1.3 60.2 + - - +
72D TYR* 3.5 10.2 - - + +
73D ASN* 2.8 46.6 + - - +
91D ILE* 4.2 27.8 - - + -
92D PRO* 4.3 11.7 - - + +
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Residues in contact with SER 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D HIS* 5.2 0.5 - - - +
29D MET* 3.6 17.6 - - - +
32D ASP* 2.8 36.2 + - - +
34D PHE* 3.3 29.9 - - - -
66D ASP 2.7 13.2 + - - -
67D SER 3.5 6.5 - - - -
69D VAL* 1.3 73.3 - - - +
71D PHE* 1.3 57.2 + - - +
73D ASN* 3.3 5.6 + - - +
74D ALA* 2.9 28.1 + - - +
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Residues in contact with PHE 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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9D LEU* 4.1 18.8 - - + -
16D LEU* 4.2 15.7 - - + -
20D ILE* 4.4 11.9 - - + -
25D ILE* 3.8 26.2 - - + -
29D MET* 4.1 5.8 - - - +
56D LEU* 4.3 8.5 - - + -
57D ILE* 5.0 8.7 - - + -
60D ILE* 3.4 35.7 - - + -
67D SER 3.1 10.8 + - - +
68D TYR* 3.3 13.7 - + - +
70D SER* 1.3 76.7 - - - +
72D TYR* 1.3 66.2 + - - +
74D ALA* 3.2 7.1 + - - +
75D LEU* 3.1 40.2 + - + +
87D LEU* 3.7 31.4 - - + -
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Residues in contact with TYR 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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68D TYR* 2.8 26.2 + - + +
69D VAL* 3.5 14.1 - - + +
71D PHE* 1.3 76.2 - - - +
73D ASN* 1.3 74.8 + - - +
75D LEU* 3.3 10.9 + - - +
76D LEU* 3.1 48.9 + - + +
84D ALA* 3.2 40.9 - - + +
87D LEU* 4.4 11.9 - - + -
88D HIS* 4.1 22.0 + - + +
91D ILE* 3.9 25.9 - - + +
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Residues in contact with ASN 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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28D HIS* 5.3 0.4 - - - -
32D ASP* 5.2 4.5 + - - +
69D VAL* 2.8 38.2 + - - +
70D SER* 3.7 5.9 - - - +
72D TYR* 1.3 88.2 - - - +
74D ALA* 1.3 66.2 + - - +
76D LEU* 3.3 10.8 + - - +
77D HIS* 3.0 49.5 + - + +
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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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25D ILE* 3.7 28.9 - - + +
28D HIS* 3.7 33.6 - - + +
29D MET* 4.9 1.1 - - + -
70D SER 2.9 13.8 + - - +
71D PHE* 3.2 11.0 + - - +
73D ASN* 1.3 77.0 - - - +
75D LEU* 1.3 62.6 + - - +
77D HIS* 3.4 0.9 + - - +
78D GLU* 3.1 28.8 + - - +
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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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16D LEU* 4.1 8.7 - - + -
20D ILE* 3.8 28.5 - - + -
25D ILE* 3.8 16.4 - - + -
71D PHE* 3.1 31.5 + - + +
72D TYR* 3.3 9.6 + - - +
74D ALA* 1.3 76.5 - - - +
76D LEU* 1.3 63.6 + - - +
78D GLU 3.3 5.7 + - - -
80D TYR* 3.0 49.3 + - + +
83D LEU* 4.5 1.3 - - + -
84D ALA* 4.4 12.8 - - + +
87D LEU* 3.7 31.2 - - + -
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Residues in contact with LEU 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 TYR* 3.1 39.1 + - + +
73D ASN* 3.7 13.9 - - - +
75D LEU* 1.3 77.9 - - - +
77D HIS* 1.3 74.8 + - + +
79D GLY* 3.1 14.7 + - - -
80D TYR 4.8 1.7 - - - +
81D LYS* 5.3 11.6 + - + -
84D ALA* 4.1 21.0 - - + +
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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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28D HIS* 4.0 23.3 + - + -
73D ASN* 3.0 42.8 + - + +
76D LEU* 1.3 87.7 - - + +
78D GLU* 1.3 64.2 + - - +
79D GLY 3.3 1.2 + - - -
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Residues in contact with GLU 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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24D TYR* 3.5 37.6 - - + -
25D ILE* 4.6 4.3 - - + -
28D HIS* 2.7 33.8 + - + +
74D ALA 3.1 18.4 + - - +
75D LEU 3.3 0.2 + - - -
76D LEU 3.2 0.4 - - - -
77D HIS* 1.3 81.1 - - - +
79D GLY* 1.3 60.8 + - - +
80D TYR* 3.4 28.8 + - + -
14F LEU* 5.0 1.7 - - - +
18F GLU* 5.2 2.9 - - - +
52F ARG* 4.7 4.7 + - - -
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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
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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