Contacts of the helix formed by residues 81 - 100 (chain D) in PDB entry 1L9X
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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18D LYS* 5.3 3.8 - - - +
76D VAL* 3.9 28.2 - - - +
77D ASP 3.2 14.3 + - - -
78D LEU* 3.7 4.8 + - - +
79D ARG 4.0 0.8 - - - -
80D ARG* 1.3 77.3 - - - +
82D ASP* 1.3 64.3 + - - +
83D TYR* 3.8 4.4 + - - -
84D ALA* 3.4 27.5 + - - +
85D LYS* 3.4 18.0 + - - +
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Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LYS* 3.0 32.7 + - - +
29D ARG* 5.1 2.3 + - - -
30D TYR* 5.3 2.4 + - - -
52D LEU* 3.9 27.5 - - + +
53D ASP* 6.1 0.2 - - - -
81D SER* 1.3 70.5 - - - +
83D TYR* 1.3 65.9 + - - +
85D LYS* 3.2 27.1 + - + +
86D VAL* 3.0 27.7 + - - +
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Residues in contact with TYR 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.0 19.1 - - + +
16D MET 3.7 17.3 - - - -
17D GLN* 3.8 21.1 - - + -
18D LYS* 5.0 0.2 - - - +
52D LEU* 3.9 18.4 - - + +
71D PHE* 3.2 25.6 - - + +
72D PRO* 2.8 35.0 + - + -
76D VAL* 4.5 6.5 - - + -
78D LEU* 3.7 21.5 - - + -
81D SER* 3.9 10.9 - - - +
82D ASP* 1.3 78.4 - - - +
84D ALA* 1.3 61.3 + - - +
86D VAL* 3.9 1.6 - - - +
87D ALA* 2.9 29.8 + - - +
111D LEU* 3.7 18.6 - - + -
112D GLY* 3.6 6.4 + - - -
115D GLU* 4.3 15.0 - - + -
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LEU* 3.4 29.8 - - + +
81D SER* 3.4 15.4 + - - +
82D ASP 3.3 0.4 - - - -
83D TYR* 1.3 81.5 - - - +
85D LYS* 1.3 58.7 + - + +
87D ALA 3.4 0.2 + - - -
88D LYS* 3.0 30.0 + - - +
115D GLU* 3.5 29.2 - - - +
118D LEU* 5.6 1.3 - - + -
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Residues in contact with LYS 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D SER 3.4 14.6 - - - +
82D ASP* 3.2 29.5 + - - +
84D ALA* 1.3 78.5 - - + +
86D VAL* 1.3 63.3 + - + +
88D LYS* 3.4 8.0 + - - +
89D ILE* 3.2 27.4 + - + +
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 3.7 23.6 - - + -
51D ARG 4.3 2.2 - - - +
52D LEU* 3.8 24.5 - - + +
59D TYR* 3.5 39.3 - - + +
82D ASP* 3.0 16.6 + - + +
83D TYR 3.9 2.7 - - - +
85D LYS* 1.3 74.8 - - + +
87D ALA* 1.3 66.4 - - - +
89D ILE* 3.1 16.7 + - + +
90D PHE* 3.1 31.4 + - + -
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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
----------------------------------------------------------
15D LEU* 3.9 10.2 - - + +
71D PHE* 3.5 28.9 - - + -
83D TYR* 2.9 20.3 + - + +
84D ALA* 3.7 2.5 - - - +
86D VAL* 1.3 76.9 - - - +
88D LYS* 1.3 58.5 + - - +
90D PHE* 3.3 0.6 + - - -
91D TYR* 2.9 30.5 + - - +
115D GLU* 3.6 30.1 - - + -
119D LEU* 4.4 2.2 - - - -
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Residues in contact with LYS 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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84D ALA 3.0 18.1 + - - +
85D LYS* 3.5 9.4 - - - +
86D VAL 3.1 0.2 - - - -
87D ALA* 1.3 77.4 - - - +
89D ILE* 1.3 63.4 + - + +
91D TYR* 3.7 1.0 - - - +
92D ASN* 3.0 44.3 + - - +
115D GLU* 4.2 0.6 + - - -
119D LEU* 3.7 30.7 - - + -
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Residues in contact with ILE 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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56D GLU* 3.4 35.9 - - + +
59D TYR* 3.8 39.3 - - + -
85D LYS* 3.2 16.8 + - + +
86D VAL* 3.1 11.5 + - + +
88D LYS* 1.3 79.1 - - + +
90D PHE* 1.3 64.8 + - + +
92D ASN* 4.0 4.5 - - - +
93D LEU* 3.0 45.0 + - + +
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 4.6 5.8 - - + -
50D VAL* 4.0 16.8 - - + -
59D TYR* 3.6 43.1 - + + -
62D LEU* 4.3 7.9 - - + -
63D PHE* 4.1 34.3 - + + -
66D ILE* 4.0 22.0 - - + -
69D ILE* 4.2 33.4 - - + -
71D PHE* 4.4 4.3 - - + -
86D VAL* 3.1 33.6 + - + +
87D ALA 3.9 5.2 - - - +
89D ILE* 1.3 78.2 - - + +
91D TYR* 1.3 66.4 + - - +
93D LEU* 3.3 5.5 + - + +
94D SER* 2.9 25.1 + - - -
104D PHE* 4.5 1.3 - + - -
106D VAL* 4.8 2.4 - - - +
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D PHE* 4.6 4.8 - - + -
87D ALA 2.9 18.1 + - - +
88D LYS 3.7 2.2 - - - +
90D PHE* 1.3 77.7 - - - +
92D ASN* 1.3 78.6 + - - +
94D SER* 2.7 26.9 + - - -
95D ILE* 3.0 36.6 + - + +
106D VAL* 4.8 7.0 - - + -
116D LEU* 4.5 10.3 - - + -
119D LEU* 3.7 43.7 - - + -
120D ILE* 3.4 32.7 - - + +
189D PHE* 3.5 17.7 - + - -
214D VAL* 4.1 15.0 - - + -
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Residues in contact with ASN 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LYS* 3.0 45.1 + - - +
89D ILE* 4.0 5.0 - - - +
91D TYR* 1.3 94.6 - - - +
93D LEU* 1.3 62.3 + - + +
95D ILE* 3.3 6.7 + - - +
96D GLN* 3.0 41.3 + - - +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLU* 5.9 0.9 - - - +
59D TYR* 4.4 1.8 - - + +
60D GLU* 4.2 30.5 - - + -
63D PHE* 3.4 44.7 - - + -
89D ILE* 3.0 40.3 + - + +
90D PHE* 3.7 6.1 - - + +
92D ASN* 1.3 76.5 - - + +
94D SER* 1.3 57.2 + - - +
96D GLN* 3.7 19.6 - - + +
97D SER* 2.9 30.3 + - - -
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Residues in contact with SER 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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63D PHE* 3.8 3.8 - - - -
90D PHE 2.9 14.3 + - - -
91D TYR* 2.7 22.7 + - - -
93D LEU* 1.3 76.9 - - - +
95D ILE* 1.3 67.4 + - - +
97D SER* 2.9 20.3 + - - -
98D PHE* 3.0 14.4 + - - +
104D PHE* 3.7 29.7 + - - +
106D VAL* 3.7 18.8 - - - +
212D TYR* 4.9 0.3 - - - -
213D PRO* 6.0 1.0 - - - +
214D VAL* 4.8 3.9 - - - +
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Residues in contact with ILE 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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91D TYR* 3.0 54.6 + - + +
92D ASN* 3.3 8.5 + - - +
94D SER* 1.3 84.6 + - - +
96D GLN* 1.3 65.2 + - + +
98D PHE* 3.3 3.8 + - - +
99D ASP* 3.1 39.3 + - - +
189D PHE* 4.3 1.6 - - + -
212D TYR* 3.6 47.6 - - + +
214D VAL* 4.7 1.3 - - + -
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Residues in contact with GLN 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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92D ASN* 3.0 32.6 + - + +
93D LEU* 3.7 22.0 - - + +
95D ILE* 1.3 79.6 - - + +
97D SER* 1.3 61.5 + - - +
99D ASP* 3.1 11.5 + - - +
100D ASP* 2.9 32.2 + - - +
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Residues in contact with SER 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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63D PHE* 3.5 19.0 - - - -
93D LEU 2.9 17.0 + - - -
94D SER* 2.9 25.1 + - - -
96D GLN* 1.3 75.1 - - - +
98D PHE* 1.3 60.6 + - - +
100D ASP* 2.9 15.8 + - - +
101D GLY 3.2 0.2 + - - -
102D ASP* 2.7 45.9 + - - +
104D PHE* 3.9 9.7 + - - +
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Residues in contact with PHE 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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94D SER 3.0 13.7 + - - +
95D ILE 3.6 4.5 - - - +
97D SER* 1.3 81.3 + - - +
99D ASP* 1.3 64.7 + - - +
101D GLY* 3.0 14.7 + - - -
102D ASP 3.2 21.0 - - - +
103D TYR* 3.8 28.0 - + - -
104D PHE 5.7 0.7 - - - +
211D LYS* 3.6 44.2 - - + -
212D TYR* 3.5 26.7 - + + -
213D PRO* 3.6 26.2 - - + -
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 3.1 22.1 + - - +
96D GLN* 3.1 10.6 + - - +
98D PHE* 1.3 80.4 - - - +
100D ASP* 1.3 60.5 + - - +
101D GLY 3.2 2.9 + - - -
211D LYS* 4.3 6.1 + - - -
212D TYR* 2.8 30.5 + - - -
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Residues in contact with ASP 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLN* 2.9 23.5 + - - +
97D SER* 2.9 12.2 + - - +
99D ASP* 1.3 80.2 - - - +
101D GLY* 1.3 58.5 + - - +
102D ASP* 3.4 3.3 + - + -
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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