Contacts of the helix formed by residues 69 - 83 (chain D) in PDB entry 4TVQ
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 LYS 69 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA 4.8 5.8 - - - +
25C VAL* 4.5 31.4 - - + -
28C PRO* 4.8 18.6 - - - -
29C VAL* 5.2 1.4 - - - +
32C GLU* 4.9 7.5 + - - -
65D LYS* 3.1 35.9 + - - +
66D ILE* 3.2 11.8 + - - +
67D LEU 3.1 1.0 - - - -
68D GLU* 1.3 85.7 + - + +
70D LYS* 1.3 61.8 + - - +
71D SER* 3.4 3.6 - - - +
72D VAL* 3.5 21.1 + - + +
73D GLU* 3.3 22.9 + - + +
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Residues in contact with LYS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 4.3 24.2 - - + -
70C LYS* 3.4 32.5 - - + +
186C LYS* 4.2 23.7 - - - +
66D ILE 4.5 2.5 - - - -
67D LEU* 3.3 18.9 + - + +
68D GLU 3.4 2.6 + - - -
69D LYS* 1.3 74.5 - - - +
71D SER* 1.3 62.3 + - - +
73D GLU* 3.1 7.6 + - - +
74D VAL* 2.9 47.5 + - + +
188D ILE* 5.8 6.7 - - - -
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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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17A MET* 5.0 5.4 - - - +
68D GLU 5.4 1.6 + - - -
69D LYS* 4.9 1.2 - - - -
70D LYS* 1.3 79.3 + - - +
72D VAL* 1.3 66.9 + - - +
74D VAL* 3.3 8.2 + - - +
75D ASN* 2.9 39.6 + - - +
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Residues in contact with VAL 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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17A MET* 4.0 43.8 + - + +
20A MET* 4.9 10.1 - - + -
24C ALA* 5.3 10.1 - - + +
25C VAL* 5.3 8.1 - - + -
69D LYS* 3.5 23.8 + - + +
70D LYS 3.3 0.6 - - - -
71D SER* 1.3 80.3 + - - +
73D GLU* 1.3 59.5 + - + +
75D ASN* 3.7 8.3 - - - +
76D PHE* 2.9 29.4 + - + +
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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
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21C PRO* 3.3 28.6 - - - +
25C VAL* 3.5 17.8 - - + +
60C GLN* 2.8 20.6 - - - +
63C ILE* 3.3 33.2 - - + +
64C MET* 3.5 10.4 - - - +
67C LEU* 4.1 16.2 - - + -
66D ILE 5.6 2.0 - - - +
69D LYS 3.3 11.9 + - - +
70D LYS 3.1 8.1 + - - +
72D VAL* 1.3 78.7 - - - +
74D VAL* 1.3 55.7 + - - +
76D PHE* 3.8 6.1 - - - -
77D THR* 2.6 38.6 + - - -
188D ILE* 5.2 0.4 - - - -
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 5.4 2.9 - - + -
70D LYS* 2.9 40.8 + - + +
71D SER* 3.7 7.6 - - - +
72D VAL 3.3 0.2 - - - -
73D GLU* 1.3 74.3 - - + +
75D ASN* 1.3 68.7 + - - +
77D THR* 3.2 2.4 + - - -
78D GLU* 2.9 28.9 + - - +
188D ILE* 4.0 36.8 - - + +
191D PHE* 5.4 6.7 - - + -
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Residues in contact with ASN 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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17A MET* 4.2 29.0 - - - +
83B MET* 3.4 27.3 - - + +
71D SER* 2.9 23.7 + - - +
72D VAL* 3.7 5.4 - - - +
74D VAL* 1.3 80.5 - - - +
76D PHE* 1.3 57.4 + - - +
78D GLU* 3.4 4.6 + - - +
79D SER* 2.9 25.9 + - - -
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Residues in contact with PHE 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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17A MET 6.1 0.6 - - - +
20A MET* 3.8 28.7 - - + -
17C MET* 2.9 50.7 - - + -
18C VAL* 4.7 1.6 - - - -
20C MET* 3.6 22.2 - - + -
21C PRO* 3.5 28.9 - - + -
60C GLN* 3.9 15.3 - - - -
72D VAL* 2.9 19.6 + - + +
73D GLU* 4.0 7.4 - - - +
74D VAL 3.2 0.2 - - - -
75D ASN* 1.3 74.4 - - - +
77D THR* 1.3 62.8 + - - +
79D SER* 2.6 25.7 + - - -
80D LEU* 2.9 24.8 + - + +
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Residues in contact with THR 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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60C GLN* 2.9 27.1 + - - +
64C MET* 3.8 8.8 - - - +
73D GLU 2.6 25.8 + - - -
74D VAL 3.2 4.2 + - - -
76D PHE* 1.3 72.7 - - - +
78D GLU* 1.3 60.7 + - - +
80D LEU* 3.3 4.2 + - - -
81D LEU* 2.9 25.1 + - - +
188D ILE* 3.9 13.5 - - + -
191D PHE* 3.8 19.5 - - + -
192D VAL* 4.1 11.9 - - + -
195D ASN* 3.3 23.2 + - - +
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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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83B MET* 3.5 8.8 - - - +
86B ASP* 2.8 27.1 - - - +
74D VAL* 2.9 19.3 + - + +
75D ASN* 3.7 8.0 - - - +
77D THR* 1.3 78.1 - - - +
79D SER* 1.3 56.5 + - - +
81D LEU* 3.1 7.5 + - - +
82D ARG* 2.4 57.0 + - - +
118D PRO* 3.4 20.2 - - + +
191D PHE* 4.0 27.4 - - + -
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Residues in contact with SER 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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79B SER* 4.5 10.3 - - - -
82B ARG* 6.2 0.2 - - - -
83B MET* 3.6 28.2 - - - -
17C MET* 3.4 18.5 - - - +
75D ASN 2.9 14.4 + - - -
76D PHE* 2.6 30.7 + - - -
78D GLU* 1.3 75.8 - - - +
80D LEU* 1.3 55.6 + - - +
82D ARG* 3.2 5.4 + - - +
83D MET* 2.8 34.5 + - - +
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Residues in contact with LEU 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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17C MET* 4.0 27.8 - - + -
18C VAL* 3.7 34.8 - - + +
60C GLN* 4.6 17.9 - - + +
76D PHE* 2.9 34.8 + - + +
77D THR 3.4 4.5 - - - +
79D SER* 1.3 77.0 + - - +
81D LEU* 1.3 62.8 + - - +
83D MET* 3.3 10.3 + - + -
84D ALA* 3.3 13.3 + - - +
195D ASN* 3.8 25.4 - - + +
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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 THR 2.9 12.4 + - - +
78D GLU* 3.1 10.1 + - - +
80D LEU* 1.3 77.9 - - - +
82D ARG* 1.3 61.4 + - - +
84D ALA* 3.3 18.3 + - - +
114D LEU 3.3 24.9 - - - +
115D SER* 3.3 11.5 - - - -
117D ILE* 4.0 4.7 - - + -
118D PRO* 3.6 22.0 - - + -
191D PHE* 3.5 40.4 - - + -
194D ALA* 3.8 13.2 - - + -
195D ASN* 3.3 15.4 + - - +
198D ILE* 3.6 24.7 - - + -
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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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82B ARG* 3.3 63.2 + - + +
83B MET* 4.0 12.8 - - - -
85B ALA* 3.8 9.3 - - - +
86B ASP* 2.8 23.3 + - - -
116B LYS* 5.1 2.8 - - - +
78D GLU* 2.4 48.5 + - - +
79D SER* 3.6 7.9 - - - +
81D LEU* 1.3 77.6 - - - +
83D MET* 1.3 58.0 + - - +
84D ALA 3.1 3.3 + - - -
85D ALA* 3.8 7.4 + - - +
115D SER* 4.1 14.1 - - - +
118D PRO* 3.3 25.0 + - + +
119D ASP* 2.4 40.2 + - - +
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Residues in contact with MET 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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75B ASN* 4.0 26.5 - - + +
78B GLU* 3.3 45.1 - - - +
79B SER* 3.9 15.7 - - - +
82B ARG* 3.7 14.4 - - - +
17C MET* 3.6 28.9 - - + -
79D SER 2.8 19.6 + - - +
80D LEU* 3.8 7.6 - - + +
81D LEU 3.2 0.6 - - - -
82D ARG* 1.3 73.0 - - - +
84D ALA* 1.3 58.6 + - - +
85D ALA 3.1 6.7 + - - -
86D ASP* 3.3 30.7 + - + +
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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
------------------------------------------------------------
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