Contacts of the helix formed by residues 78 - 92 (chain D) in PDB entry 3LUE
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 ASN 78 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ARG* 4.4 15.6 - - - +
69D TYR* 2.7 44.0 + - - +
70D PRO* 3.6 14.6 + - + +
76D VAL* 3.5 10.5 - - - +
77D THR* 1.3 83.8 + - - +
79D TRP* 1.3 59.8 + - - +
80D ASP* 3.9 3.9 + - - +
81D ASP* 3.0 8.1 + - - +
82D MET* 3.1 20.1 + - - +
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Residues in contact with TRP 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 3.7 43.5 + - + -
77D THR 4.1 4.9 + - - -
78D ASN* 1.3 74.1 - - - +
80D ASP* 1.3 64.3 + - - +
82D MET* 3.6 5.0 + - + +
83D GLU* 3.0 29.9 + - - +
86D TRP* 4.1 20.0 - + - -
115D ASN* 4.1 34.1 - - + +
118D LYS* 3.4 47.9 - - + +
119D MET* 4.2 12.8 - - + -
122D ILE* 3.5 28.9 - - + -
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU 4.4 11.8 - - - +
68D LYS* 5.2 0.9 - - - -
69D TYR* 1.3 66.1 - - + +
78D ASN* 3.6 4.8 + - - +
79D TRP* 1.3 78.3 - - - +
81D ASP* 1.3 46.5 - - - +
83D GLU* 4.0 13.3 - - + +
84D LYS* 5.0 0.2 - - - -
118D LYS* 5.7 0.5 + - - -
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Residues in contact with ASP 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D ILE* 1.7 51.4 - - + +
62D ARG* 4.8 0.3 + - - -
67D LEU* 3.2 31.2 - - - +
69D TYR* 0.4 440.4 + - + +
78D ASN* 2.9 10.2 + - - +
80D ASP* 1.3 65.1 - - - +
82D MET* 1.3 52.3 + - - +
84D LYS* 3.4 0.3 - - - +
85D ILE* 3.1 15.1 + - - +
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Residues in contact with MET 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASN* 3.2 27.8 - - - +
17D CYS* 4.7 0.4 - - - -
69D TYR* 2.3 2.0 - - - -
70D PRO* 3.8 7.5 - - + +
71D ILE* 3.4 37.2 - - + -
76D VAL* 3.5 23.6 - - + -
78D ASN 3.1 19.9 + - - +
79D TRP* 3.9 8.1 - - + +
81D ASP* 1.3 73.6 - - - +
83D GLU* 1.3 63.1 + - - +
85D ILE* 2.8 43.8 + - + +
86D TRP* 3.1 49.5 + - + +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR* 2.8 21.0 - - + +
79D TRP 3.0 20.7 + - - +
80D ASP* 3.3 10.7 - - + +
82D MET* 1.3 73.8 - - - +
84D LYS* 1.3 64.5 + - - +
86D TRP* 3.3 10.8 + - - +
87D HIS* 3.1 20.8 + - - +
118D LYS* 4.5 6.4 + - - -
122D ILE* 3.9 36.6 - - + +
126D THR* 3.9 22.4 + - - +
127D PHE* 4.0 6.7 - - + -
120O LYS* 5.4 7.4 - - - +
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Residues in contact with LYS 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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34D ILE* 2.7 26.2 - - + +
35D VAL* 2.6 19.6 + - - +
67D LEU 2.9 5.4 - - - -
68D LYS* 0.4 254.6 + - + +
69D TYR* 0.8 212.1 - - + +
83D GLU* 1.3 64.6 - - - +
85D ILE* 1.3 63.3 + - - +
86D TRP 3.2 0.3 + - - -
87D HIS 3.3 0.5 + - - -
88D HIS* 3.0 20.3 + - - +
122O VAL* 3.4 14.5 - - + +
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Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D CYS* 3.9 17.0 - - - -
31D PHE* 4.0 12.7 - - + -
32D PRO 5.1 1.3 - - - +
33D SER* 4.2 30.5 - - - +
34D ILE* 5.1 12.8 - - + +
69D TYR* 4.8 0.4 - - + -
70D PRO* 3.6 27.6 - - + -
71D ILE* 5.0 0.2 - - + -
81D ASP 3.1 10.3 + - - +
82D MET* 2.8 33.6 + - + +
84D LYS* 1.3 75.1 - - - +
86D TRP* 1.3 61.2 + - + +
88D HIS* 3.2 8.7 + - - +
89D THR* 2.8 32.2 + - - +
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Residues in contact with TRP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 3.7 19.7 - - + +
12D ASN* 2.9 37.0 + - - -
17D CYS* 6.2 0.2 - - - -
76D VAL* 5.6 1.3 - - + -
79D TRP* 4.1 16.6 - + - -
82D MET* 3.1 48.3 + - + +
83D GLU* 3.8 7.0 - - - +
85D ILE* 1.3 77.1 - - + +
87D HIS* 1.3 63.8 + - - +
89D THR* 2.8 28.7 + - - -
90D PHE* 3.1 15.1 + + + -
105D LEU* 4.4 11.2 - - + +
119D MET* 4.2 27.8 - - + -
122D ILE* 4.1 20.9 - - + -
123D MET* 3.5 28.9 - - + -
127D PHE* 3.9 11.9 - + + -
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Residues in contact with HIS 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR 4.6 2.5 - - - +
83D GLU 3.1 12.7 + - - +
84D LYS* 3.4 8.5 - - - +
86D TRP* 1.3 73.7 - - - +
88D HIS* 1.3 59.1 + - - +
90D PHE* 4.5 0.7 - - - -
91D TYR* 2.9 76.3 + + + +
92D ASN* 5.4 2.5 - - - -
127D PHE* 3.7 18.0 - - + -
118O GLY 5.6 1.1 - - - -
119O VAL* 4.5 8.7 - - + -
120O LYS* 4.0 44.1 + - + +
122O VAL* 4.2 8.7 - - + -
143O THR* 4.1 19.3 - - + +
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Residues in contact with HIS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D PHE* 4.2 22.9 - + - +
84D LYS 3.0 13.0 + - - +
85D ILE* 3.3 10.1 - - - +
87D HIS* 1.3 72.8 - - - +
89D THR* 1.3 58.1 + - - +
92D ASN* 3.0 44.2 + - + +
93D GLU* 2.7 65.7 + - - +
122O VAL* 4.3 18.5 + - + +
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Residues in contact with THR 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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10D VAL* 3.9 22.3 - - + +
17D CYS* 5.7 0.2 - - - -
19D ALA* 3.7 31.0 - - + -
31D PHE* 3.5 16.8 - - + -
85D ILE* 2.8 17.9 + - - +
86D TRP* 2.8 27.1 + - - -
88D HIS* 1.3 72.6 - - - +
90D PHE* 1.3 58.6 + - + +
93D GLU* 3.3 8.7 + - - +
94D LEU* 2.7 41.2 + - + +
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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
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8D LEU* 3.3 35.0 - - + -
10D VAL* 4.5 17.3 - - + -
86D TRP* 3.1 30.9 + + + -
87D HIS* 4.1 1.6 - - - +
89D THR* 1.3 78.2 - - + +
91D TYR* 1.3 62.2 + + + +
94D LEU* 4.8 0.4 - - + -
95D ARG 2.8 31.2 + - - -
96D VAL* 2.8 22.9 + - + +
98D PRO* 3.6 32.3 - - + -
103D VAL* 4.0 17.7 - - + -
123D MET* 4.0 31.2 - - + -
127D PHE* 4.2 18.8 - + - -
142O TRP* 3.6 0.7 - - - -
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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
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87D HIS* 2.9 70.2 + + + +
90D PHE* 1.3 65.8 - - + +
92D ASN* 1.3 65.6 + - - +
96D VAL 4.0 0.4 - - - -
98D PRO* 3.7 24.1 - - + +
99D GLU* 4.8 3.6 + - - -
127D PHE* 4.1 20.1 + + - -
142O TRP* 1.2 58.7 - - + +
143O THR* 4.6 6.1 - - + +
146O LEU* 1.0 129.8 - - + +
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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
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87D HIS* 5.4 2.8 - - - -
88D HIS* 3.0 43.4 + - + +
90D PHE 3.4 0.2 - - - -
91D TYR* 1.3 96.1 + - - +
93D GLU* 1.3 71.4 + - - +
95D ARG* 3.5 17.8 - - - +
43O TRP* 4.6 4.9 - - - -
47O GLN* 4.3 4.5 + - - +
122O VAL* 5.0 5.9 - - - +
124O ILE* 4.2 13.5 - - - +
139O GLY* 2.7 44.8 + - - -
142O TRP* 3.7 0.7 - - - -
143O THR* 3.3 10.4 + - - -
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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