Contacts of the helix formed by residues 67 - 85 (chain D) in PDB entry 4UC5
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 67 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ILE* 3.7 5.3 - - - +
66D HIS* 1.3 97.7 - - + +
68D PRO* 1.3 74.7 - - - +
69D LYS* 3.1 19.7 + - - +
70D ALA* 3.4 23.9 + - + +
71D ALA* 3.2 19.6 + - - +
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Residues in contact with PRO 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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65D ILE* 4.4 0.2 - - - -
66D HIS 4.5 2.2 - - - +
67D ASP* 1.3 89.3 - - - +
69D LYS* 1.3 59.0 + - - +
70D ALA 3.3 0.2 - - - -
71D ALA* 3.6 8.7 - - + +
72D LEU* 2.9 37.9 + - + +
109D LEU* 4.6 11.7 - - + -
127D GLN* 3.7 41.1 - - + +
131D LEU* 4.1 23.5 - - + +
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASP* 3.1 14.5 + - - +
68D PRO* 1.3 78.4 - - - +
70D ALA* 1.3 62.9 + - - +
72D LEU* 3.4 9.1 + - - +
73D GLU* 3.0 23.3 + - - +
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Residues in contact with ALA 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 HIS* 6.3 1.8 - - + -
67D ASP* 3.4 24.9 + - + +
69D LYS* 1.3 79.5 - - - +
71D ALA* 1.3 53.6 + - - +
73D GLU* 3.3 10.8 + - - +
74D TYR* 2.7 35.4 + - - +
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Residues in contact with ALA 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D PRO* 5.8 2.7 - - - -
65D ILE* 4.0 26.5 - - + -
67D ASP 3.2 14.9 + - - +
68D PRO* 3.6 9.9 - - + +
70D ALA* 1.3 80.1 - - - +
72D LEU* 1.3 55.7 + - - +
74D TYR* 3.3 7.5 + - - +
75D ALA* 2.9 29.2 + - - +
93D MET* 3.6 12.9 - - + +
131D LEU* 4.2 13.5 - - + -
135D LEU* 5.0 1.6 - - - -
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Residues in contact with LEU 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 PRO* 2.9 26.7 + - + +
69D LYS* 3.8 7.4 - - - +
71D ALA* 1.3 71.7 - - - +
73D GLU* 1.3 66.3 + - - +
75D ALA* 3.2 5.4 + - - +
76D GLU* 3.0 22.5 + - - +
131D LEU* 3.9 17.5 - - + -
134D SER* 3.8 27.1 - - - +
135D LEU* 4.2 6.7 - - + -
138D MET* 3.3 33.4 - - + +
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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
----------------------------------------------------------
69D LYS 3.0 17.8 + - - +
70D ALA* 3.7 8.5 - - - +
72D LEU* 1.3 73.9 - - - +
74D TYR* 1.3 65.0 + - - +
76D GLU* 3.3 9.0 + - + +
77D ARG* 3.3 50.0 + - + +
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Residues in contact with TYR 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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60D ILE* 3.8 17.1 - - - +
61D GLY* 3.6 28.4 - - - -
62D PRO* 4.4 17.5 - - + -
70D ALA 2.7 21.8 + - - +
71D ALA* 3.4 9.4 - - - +
73D GLU* 1.3 72.2 - - - +
75D ALA* 1.3 60.1 + - - +
77D ARG* 3.2 11.8 + - - +
78D LEU* 2.9 51.6 + - + +
93D MET* 4.1 17.9 - - + -
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Residues in contact with ALA 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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71D ALA 2.9 9.3 + - - +
72D LEU 3.4 8.3 - - - +
73D GLU 3.2 0.2 - - - -
74D TYR* 1.3 77.8 - - - +
76D GLU* 1.3 52.4 + - - +
78D LEU* 3.1 4.4 + - - +
79D LEU* 2.7 36.4 + - - +
93D MET* 3.7 12.3 - - - -
135D LEU* 3.3 34.5 - - + -
138D MET* 3.9 12.3 - - - -
140D MET* 4.0 8.5 - - + +
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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 LEU 3.0 13.1 + - - +
73D GLU* 3.7 11.9 - - + +
74D TYR 3.3 0.2 - - - -
75D ALA* 1.3 77.7 - - - +
77D ARG* 1.3 60.8 + - + +
79D LEU* 3.5 18.6 + - - +
80D LYS* 3.7 6.9 + - - +
138D MET* 4.2 10.0 - - + -
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Residues in contact with ARG 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 GLU* 3.3 39.5 + - + +
74D TYR* 3.2 10.7 + - + +
76D GLU* 1.3 75.3 - - + +
78D LEU* 1.3 65.8 + - - +
80D LYS* 3.3 18.8 + - - +
81D LEU* 3.8 9.6 + - - +
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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
----------------------------------------------------------
60D ILE* 3.9 30.5 - - + +
74D TYR* 2.9 39.8 + - + +
75D ALA 3.6 7.4 - - - +
77D ARG* 1.3 75.0 - - - +
79D LEU* 1.3 67.3 + - - +
81D LEU* 3.0 17.1 + - + +
82D ARG* 2.9 19.8 + - - +
91D ILE* 3.8 31.2 - - + -
93D MET* 4.1 8.5 - - + -
140D MET* 3.8 23.3 - - + -
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Residues in contact with LEU 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 ALA 2.7 20.4 + - - +
76D GLU* 3.6 11.2 - - - +
77D ARG 3.3 0.2 - - - -
78D LEU* 1.3 72.6 - - - +
80D LYS* 1.3 61.7 + - - +
82D ARG* 3.4 9.6 + - + +
83D LYS* 3.1 24.6 + - + +
138D MET* 3.4 30.1 - - + +
139D GLY* 3.4 32.3 - - - +
140D MET* 3.5 15.7 - - + +
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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 GLU 3.7 6.9 + - - +
77D ARG* 3.3 12.2 + - - +
78D LEU 3.0 1.0 + - - -
79D LEU* 1.3 80.5 - - - +
81D LEU* 1.3 63.5 + - + +
83D LYS* 3.7 5.2 + - - +
84D GLN* 3.1 26.3 + - - +
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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
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77D ARG 4.2 10.3 - - - +
78D LEU* 3.0 17.0 + - + +
80D LYS* 1.3 79.6 - - + +
82D ARG* 1.3 60.4 + - - +
84D GLN* 3.6 24.5 - - - +
85D TYR* 2.8 58.6 + - + +
91D ILE* 4.0 9.4 - - + +
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Residues in contact with ARG 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 LEU* 3.8 11.9 - - - +
40D ARG* 3.7 30.7 - - - +
41D THR* 4.6 2.2 + - - -
44D GLU* 5.1 0.2 + - - -
78D LEU 2.9 11.7 + - - +
79D LEU* 3.4 16.9 - - + +
81D LEU* 1.3 77.8 - - - +
83D LYS* 1.3 60.2 + - - +
85D TYR 4.1 0.7 - - - -
86D GLU* 3.4 24.1 + - - +
89D LEU 4.8 2.3 - - - +
90D LEU* 3.5 24.1 - - - +
91D ILE* 2.9 50.6 + - + +
139D GLY 3.4 14.6 + - - -
140D MET* 3.7 20.4 - - + -
141D PRO* 3.4 20.6 - - - +
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Residues in contact with LYS 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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79D LEU* 3.1 15.4 + - + +
80D LYS* 3.9 5.6 - - - +
82D ARG* 1.3 78.8 - - - +
84D GLN* 1.3 65.8 + - - +
86D GLU* 3.3 51.2 + - - +
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Residues in contact with GLN 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 LYS 3.1 18.9 + - - +
81D LEU* 3.2 22.1 + - - +
83D LYS* 1.3 78.9 - - - +
85D TYR* 1.3 92.7 + - + +
86D GLU* 3.4 3.3 + - - +
87D ASN* 5.1 3.5 + - - +
88D GLU* 4.7 2.9 - - - +
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Residues in contact with TYR 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* 2.8 57.1 + - + +
82D ARG 4.1 2.0 - - - -
84D GLN* 1.3 100.7 + - + +
86D GLU* 1.3 58.8 + - - +
87D ASN 3.2 2.9 - - - -
88D GLU* 3.0 19.3 + - + +
89D LEU* 2.8 61.6 + - + +
91D ILE* 4.5 4.5 - - + -
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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