Contacts of the helix formed by residues 59 - 75 (chain D) in PDB entry 3UGV
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 ALA 59 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PRO* 5.1 5.8 - - + +
56D VAL* 2.8 30.1 + - + +
58D LYS* 1.3 76.8 - - - +
60D MET* 1.3 57.5 + - - +
61D LYS 3.1 0.2 - - - -
62D TYR* 2.7 45.4 + - + +
63D LEU* 3.0 26.0 + - + +
100D LEU* 4.7 7.9 - - + -
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Residues in contact with MET 60 (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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14D PRO* 3.8 25.4 - - + -
15D VAL 3.6 19.3 - - - +
16D LEU* 5.0 4.9 - - + -
34D PRO* 3.9 21.1 - - + -
35D LEU 3.7 14.6 - - - +
36D ILE* 3.7 39.7 - - + -
54D PRO* 4.1 10.8 - - + -
57D PRO* 3.2 23.4 + - + +
59D ALA* 1.3 77.8 - - - +
61D LYS* 1.3 58.7 + - + +
62D TYR 3.1 0.2 - - - -
63D LEU* 4.3 0.9 - - - +
64D VAL* 2.8 35.8 + - + +
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Residues in contact with LYS 61 (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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57D PRO 5.0 2.2 - - - +
58D LYS* 3.6 47.0 + - + +
59D ALA 3.1 1.0 - - - -
60D MET* 1.3 78.0 - - + +
62D TYR* 1.3 72.9 + - + +
64D VAL* 5.4 0.2 - - - -
65D PRO* 3.2 22.7 - - - +
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Residues in contact with TYR 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL* 6.3 0.7 - - + -
58D LYS* 3.6 27.6 + - - +
59D ALA* 2.7 27.0 + - + +
61D LYS* 1.3 98.0 + - + +
63D LEU* 1.3 63.9 + - - +
65D PRO* 3.9 5.4 - - - +
66D ALA* 3.4 21.1 + - - +
100D LEU* 4.1 30.7 - - + -
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Residues in contact with LEU 63 (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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36D ILE* 3.8 21.5 - - + -
52D LEU* 5.1 2.2 - - + -
54D PRO* 3.9 28.5 - - + -
59D ALA* 3.0 20.8 + - + +
60D MET 3.2 0.6 + - - +
62D TYR* 1.3 77.4 - - - +
64D VAL* 1.3 61.1 + - - +
66D ALA* 3.0 5.8 + - + +
67D LEU* 2.8 36.8 + - + +
100D LEU* 3.7 46.0 - - + +
103D ILE* 4.0 22.2 - - + -
104D ALA* 4.1 13.2 - - + +
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Residues in contact with VAL 64 (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 ALA* 3.8 18.4 - - + +
14D PRO* 4.3 29.4 - - + -
36D ILE* 4.6 11.9 - - + -
60D MET* 2.8 24.7 + - + +
61D LYS* 5.4 0.2 - - - -
63D LEU* 1.3 71.1 - - - +
65D PRO* 1.3 70.8 - - + +
66D ALA 3.2 0.2 + - - -
67D LEU* 3.2 9.1 + - - +
68D HIS* 3.0 48.8 + - + +
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Residues in contact with PRO 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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61D LYS* 3.2 31.0 - - - +
62D TYR* 3.9 4.3 - - - +
63D LEU 3.8 0.7 - - - -
64D VAL* 1.3 98.7 - - + +
66D ALA* 1.3 56.7 + - - +
68D HIS* 3.9 6.1 - - + +
69D ASP* 3.0 36.5 + - - +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D TYR 3.4 16.2 + - - +
63D LEU* 3.0 10.7 + - + +
65D PRO* 1.3 76.4 - - - +
67D LEU* 1.3 61.9 + - - +
69D ASP* 3.4 9.2 + - - +
70D MET* 3.1 32.0 + - - +
92D LEU* 5.2 11.4 - - + -
100D LEU 5.9 0.4 - - - +
104D ALA* 4.2 17.5 - - + -
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Residues in contact with LEU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.1 17.7 - - + +
12D ALA* 3.6 24.2 - - + -
36D ILE* 3.9 17.9 - - + -
38D ILE* 4.1 19.7 - - + -
52D LEU* 4.6 8.3 - - + -
63D LEU* 2.8 26.3 + - + +
64D VAL* 3.6 4.0 - - - +
66D ALA* 1.3 75.7 - - - +
68D HIS* 1.3 59.8 + - - +
70D MET* 3.0 7.8 + - - +
71D SER* 2.8 26.7 + - - -
104D ALA* 3.5 33.4 - - + +
107D GLY* 5.0 0.4 - - - -
108D VAL* 3.9 16.4 - - + -
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Residues in contact with HIS 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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10D LEU* 3.5 22.6 + - + -
11D THR* 4.0 6.0 - - + +
12D ALA* 3.2 31.9 + - + +
64D VAL* 3.0 41.0 + - + +
65D PRO* 4.1 5.9 - - + +
67D LEU* 1.3 78.3 - - - +
69D ASP* 1.3 62.6 + - - +
71D SER* 3.3 5.9 + - - -
72D ASP* 3.0 29.5 + - - +
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Residues in contact with ASP 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 PRO* 3.0 24.8 + - - +
66D ALA* 3.7 8.7 - - - +
68D HIS* 1.3 78.6 - - - +
70D MET* 1.3 60.7 + - + +
72D ASP* 3.4 15.0 + - - +
73D MET* 3.1 22.9 + - - +
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Residues in contact with MET 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 ALA 3.1 14.1 + - - +
67D LEU* 3.0 10.6 + - - +
69D ASP* 1.3 73.4 - - + +
71D SER* 1.3 67.2 + - - +
73D MET* 3.2 8.7 + - + -
74D LEU* 2.9 37.2 + - + +
88D THR* 3.8 39.3 - - + +
91D SER* 4.7 6.3 - - - +
92D LEU* 3.8 26.7 - - + -
101D SER 4.2 2.7 - - - +
104D ALA* 3.6 32.8 - - + -
105D ALA* 3.8 8.5 - - + +
108D VAL* 3.9 24.5 - - + -
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Residues in contact with SER 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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7D PHE* 3.7 14.9 - - - -
8D ARG 5.0 0.2 - - - +
9D LYS* 3.5 10.6 - - - +
10D LEU* 2.8 45.3 + - - +
67D LEU 2.8 12.0 + - - -
68D HIS* 3.3 13.7 - - - -
70D MET* 1.3 76.3 - - - +
72D ASP* 1.3 65.5 + - - +
74D LEU 3.1 1.0 + - - -
75D ALA* 3.0 23.4 + - - +
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Residues in contact with ASP 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 HIS* 3.0 21.6 + - - +
69D ASP* 3.7 17.5 - - - +
70D MET 3.3 0.2 - - - -
71D SER* 1.3 79.0 + - - +
73D MET* 1.3 61.8 + - - +
74D LEU 3.5 0.2 + - - -
75D ALA* 3.6 17.3 + - - +
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Residues in contact with MET 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 ASP 3.1 17.8 + - - +
70D MET* 3.7 8.1 - - + +
72D ASP* 1.3 77.5 - - - +
74D LEU* 1.3 93.9 + - + +
75D ALA 4.7 1.2 - - - +
77D GLN* 2.9 16.3 + - - +
87D LYS* 4.0 24.9 - - + +
88D THR* 4.3 8.5 - - + -
91D SER* 3.8 27.8 - - - +
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Residues in contact with LEU 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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7D PHE* 3.7 35.0 - - + +
10D LEU* 5.8 0.4 - - + -
70D MET* 2.9 29.5 + - + +
73D MET* 1.3 97.0 - - + +
75D ALA* 1.3 65.2 + - - +
76D GLY 3.3 0.5 + - - -
77D GLN* 2.9 41.3 + - + +
84D ILE* 3.8 42.6 - - + -
87D LYS* 4.5 11.4 - - + +
88D THR* 4.2 7.9 - - + -
108D VAL* 4.1 15.7 - - + -
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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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7D PHE* 3.8 10.3 - - - -
8D ARG 3.9 13.2 - - - +
71D SER 3.0 11.5 + - - +
72D ASP* 3.7 16.9 - - - +
73D MET 3.5 2.6 - - - +
74D LEU* 1.3 77.8 - - - +
76D GLY* 1.3 58.8 + - - +
77D GLN* 3.3 7.1 + - - +
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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