Contacts of the helix formed by residues 81 - 100 (chain D) in PDB entry 4YYJ
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 SER 81 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 4.0 12.1 - - - +
29D LEU* 4.5 0.7 - - - +
79D TYR* 3.4 6.2 - - - +
80D LYS* 1.3 81.6 - - - +
82D VAL* 1.3 65.3 + - - +
83D THR* 3.6 11.6 + - - -
84D GLU* 3.3 34.8 + - - +
85D PHE* 3.4 10.9 + - - +
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Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLN* 3.9 15.6 + - - +
25D ILE* 4.0 4.8 - - + +
28D LEU* 3.7 30.3 - - + -
29D LEU* 4.0 17.9 - - + -
32D PHE* 3.9 19.3 - - + -
81D SER* 1.3 75.6 - - - +
83D THR* 1.3 57.7 + - - +
85D PHE* 3.2 2.6 + - + +
86D LYS* 2.9 53.2 + - + +
121D MET* 4.7 3.1 - - - +
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Residues in contact with THR 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D SER* 3.1 11.9 + - - +
82D VAL* 1.3 79.9 - - - +
84D GLU* 1.3 59.5 + - + +
86D LYS* 3.4 13.4 - - - +
87D ALA* 3.0 27.7 + - + +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLU 3.5 6.8 - - - +
79D TYR* 3.5 23.5 - - + -
80D LYS* 2.7 37.3 + - - +
81D SER* 3.3 21.2 + - - +
82D VAL 3.2 0.8 - - - -
83D THR* 1.3 77.2 - - + +
85D PHE* 1.3 65.1 + - - +
87D ALA* 3.4 7.6 + - - +
88D ASP* 3.3 16.3 + - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 3.7 44.9 - - + -
32D PHE* 3.8 12.3 - + + -
33D LEU* 4.2 16.8 - - + -
36D LEU* 4.1 9.2 - - + -
70D MET* 3.3 37.3 - - + +
74D ILE* 4.0 20.4 - - + -
79D TYR* 3.7 28.4 - + + -
81D SER 3.4 4.9 + - - +
82D VAL 3.2 7.8 + - - +
84D GLU* 1.3 75.1 - - - +
86D LYS* 1.3 69.0 + - + +
88D ASP 3.0 2.8 + - - -
89D PHE* 3.0 20.1 + - + +
121D MET* 3.7 29.8 - - + -
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D VAL* 2.9 32.0 + - + +
83D THR* 3.4 14.4 - - - +
85D PHE* 1.3 79.0 - - - +
87D ALA* 1.3 57.1 + - - +
89D PHE* 3.3 7.9 + - - +
90D LYS 2.9 23.9 + - - -
118D PHE* 3.6 44.1 + - + -
121D MET* 2.9 54.3 + - + -
122D SER* 3.3 15.4 + - - -
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Residues in contact with ALA 87 (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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83D THR* 3.0 17.0 + - + +
84D GLU* 3.8 8.3 - - - +
85D PHE 3.2 0.4 - - - -
86D LYS* 1.3 77.0 - - - +
88D ASP* 1.3 58.5 + - - +
90D LYS* 3.4 9.2 + - - +
91D LEU* 2.9 28.6 + - - +
118D PHE* 5.3 0.2 - - - -
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Residues in contact with ASP 88 (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* 3.5 30.0 - - - +
70D MET* 4.0 9.2 - - + -
73D LYS* 2.8 28.9 + - - +
79D TYR* 2.5 33.5 + - - +
84D GLU 3.3 8.2 + - - +
85D PHE 3.0 8.3 + - - +
87D ALA* 1.3 75.0 - - - +
89D PHE* 1.3 66.0 + - - +
91D LEU* 3.3 14.1 + - - +
92D MET* 3.0 18.5 + - - +
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Residues in contact with PHE 89 (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 LEU* 3.8 32.8 - - + -
67D PHE* 4.2 8.5 - + - -
70D MET* 3.6 15.1 - - + +
85D PHE* 3.0 12.2 + - + +
86D LYS* 3.5 9.0 - - - +
88D ASP* 1.3 77.0 - - - +
90D LYS* 1.3 61.2 + - - +
92D MET* 3.1 30.1 + - + +
93D CYS* 3.0 33.9 + - - -
113D ILE* 3.3 36.6 - - + -
114D LEU* 3.9 15.0 - - + -
117D GLY* 3.9 13.0 - - - -
118D PHE* 3.8 18.4 - + - -
121D MET* 3.9 12.1 - - + -
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Residues in contact with LYS 90 (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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86D LYS 2.9 14.8 + - - +
87D ALA* 3.6 10.5 - - - +
89D PHE* 1.3 74.1 - - - +
91D LEU* 1.3 57.0 + - - +
93D CYS* 3.3 1.4 + - - +
94D ASP* 2.6 71.6 + - - +
114D LEU* 4.0 19.3 - - + -
118D PHE* 3.9 19.5 - - + -
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Residues in contact with LEU 91 (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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63D HIS* 3.6 35.2 - - + +
65D MET* 4.2 14.1 - - + -
87D ALA 2.9 17.0 + - - +
88D ASP* 3.5 20.6 - - - +
89D PHE 3.3 0.2 - - - -
90D LYS* 1.3 76.4 - - - +
92D MET* 1.3 57.2 + - - +
94D ASP* 4.4 7.4 - - + -
95D ASN* 2.9 54.4 + - - +
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Residues in contact with MET 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D PHE* 3.6 37.6 - - + -
65D MET* 3.5 31.0 - - + +
66D ASP* 3.6 22.2 - - - -
67D PHE* 3.7 39.3 - - + -
70D MET* 4.6 2.7 - - - +
88D ASP 3.0 13.4 + - - +
89D PHE* 3.1 28.2 + - + +
91D LEU* 1.3 77.5 - - - +
93D CYS* 1.3 65.5 + - - +
95D ASN* 3.5 5.1 + - - +
96D ALA* 3.2 21.0 + - - +
113D ILE* 4.7 0.9 - - + -
8F BTK 5.6 0.2 - - - +
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Residues in contact with CYS 93 (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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45D PHE* 4.7 1.8 - - - -
89D PHE* 3.0 47.3 + - - +
90D LYS 3.8 2.9 - - - +
92D MET* 1.3 82.1 - - - +
94D ASP* 1.3 57.6 + - - +
96D ALA* 3.2 5.1 + - - +
97D MET* 3.0 33.1 + - - +
110D ALA* 3.7 26.1 - - - +
113D ILE* 4.0 8.5 - - - -
114D LEU* 3.8 29.2 - - + -
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Residues in contact with ASP 94 (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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90D LYS* 2.6 65.9 + - - +
91D LEU* 3.8 8.3 + - + +
93D CYS* 1.3 69.0 - - - +
95D ASN* 1.3 59.4 + - - +
97D MET* 3.7 22.2 - - - +
98D THR* 2.7 40.2 + - - +
114D LEU* 4.0 7.1 - - - +
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Residues in contact with ASN 95 (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 TYR* 3.9 16.9 + - - +
61D ILE* 3.5 37.9 - - + +
62D LYS 5.4 0.2 + - - -
63D HIS 2.9 25.9 + - - +
64D PRO* 3.7 7.7 - - - +
65D MET 3.7 7.7 + - - +
91D LEU* 2.9 40.0 + - - +
92D MET* 3.7 6.1 - - - +
94D ASP* 1.3 73.0 - - - +
96D ALA* 1.3 59.9 + - - +
98D THR* 3.2 1.4 + - - -
99D TYR* 2.9 29.0 + - - +
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Residues in contact with ALA 96 (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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45D PHE* 3.9 14.4 - - + -
57D TYR* 5.0 0.4 + - - -
92D MET 3.2 9.8 + - - +
93D CYS 3.2 3.9 + - - +
95D ASN* 1.3 79.0 - - - +
97D MET* 1.3 58.6 + - - +
100D ASN* 2.9 44.2 + - - +
106D TYR 4.5 1.6 - - - +
107D TYR* 4.5 2.4 - - - -
110D ALA* 3.5 26.2 - - + -
8F BTK 4.0 16.8 - - + -
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Residues in contact with MET 97 (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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93D CYS 3.0 16.8 + - - +
94D ASP* 3.7 27.6 - - - +
96D ALA* 1.3 75.6 - - - +
98D THR* 1.3 63.2 + - - +
100D ASN 3.7 3.6 - - - +
107D TYR* 3.5 47.2 - - + +
110D ALA* 4.0 12.6 - - + +
111D LYS* 3.6 38.1 - - - -
114D LEU* 3.8 17.9 - - + -
115D HIS* 6.2 0.9 - - + -
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Residues in contact with THR 98 (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* 4.3 13.0 - - + +
61D ILE* 4.2 15.7 - - + -
94D ASP* 2.7 24.7 + - - +
95D ASN* 3.6 4.0 - - - -
97D MET* 1.3 80.5 - - - +
99D TYR* 1.3 55.8 + - - +
100D ASN 4.6 0.9 - - - +
101E ARG* 2.6 37.2 + - - +
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Residues in contact with TYR 99 (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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54D ALA* 3.1 33.0 - - + -
55D PRO 2.6 30.3 + - - -
57D TYR* 3.7 35.7 - + + -
60D ILE* 3.9 29.2 - - + -
61D ILE* 4.3 6.1 - - + -
95D ASN 2.9 16.0 + - - +
98D THR* 1.3 82.2 - - - +
100D ASN* 1.3 82.1 + - - +
101D ARG 3.8 1.2 + - - -
101E ARG* 3.6 25.0 + - - +
6F GLY 3.7 1.2 + - - -
7F GLY* 3.4 28.2 - - - -
8F BTK 4.2 5.2 - - + -
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Residues in contact with ASN 100 (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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96D ALA* 2.9 28.9 + - - +
97D MET 3.7 5.2 - - - +
98D THR 4.6 1.0 - - - +
99D TYR* 1.3 92.5 - - - +
101D ARG* 1.3 65.2 + - - +
102D PRO* 3.6 1.4 - - - +
104D THR* 3.5 16.4 - - + +
106D TYR* 3.5 28.7 - - + +
107D TYR* 3.3 19.6 - - - +
101E ARG* 5.7 0.9 - - - -
7F GLY* 5.4 0.3 - - - -
8F BTK 2.9 43.9 + - - +
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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
------------------------------------------------------------
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