Contacts of the helix formed by residues 78 - 92 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ARG* 4.4 15.8 - - - +
69G TYR* 2.7 44.4 + - - +
70G PRO* 3.6 14.0 + - + +
76G VAL* 3.5 10.4 - - - +
77G THR* 1.3 82.8 + - - +
79G TRP* 1.3 59.3 + - - +
80G ASP* 3.9 3.6 + - - +
81G ASP* 3.0 7.6 + - - +
82G MET* 3.1 19.9 + - - +
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Residues in contact with TRP 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G VAL* 3.7 43.2 + - + -
77G THR 4.1 5.4 + - - -
78G ASN* 1.3 73.9 - - - +
80G ASP* 1.3 64.9 + - - +
82G MET* 3.6 5.7 + - + +
83G GLU* 3.0 29.5 + - - +
86G TRP* 4.1 20.2 - + - -
115G ASN* 4.1 34.4 - - + +
118G LYS* 3.4 47.7 - - + +
119G MET* 4.2 12.8 - - + -
122G ILE* 3.5 28.9 - - + -
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Residues in contact with ASP 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G LEU 4.4 10.7 - - - +
68G LYS* 5.2 1.1 - - - -
69G TYR* 1.3 67.7 - - + +
78G ASN* 3.6 4.2 + - - -
79G TRP* 1.3 77.5 + - - +
81G ASP* 1.3 47.4 - - - +
83G GLU* 4.0 13.0 - - + +
118G LYS* 5.8 0.3 + - - -
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Residues in contact with ASP 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ILE* 1.7 51.4 - - + +
62G ARG* 4.8 0.2 + - - -
67G LEU* 3.2 31.6 - - - +
69G TYR* 0.4 442.0 + - + +
78G ASN* 2.9 9.3 + - - +
80G ASP* 1.3 65.9 - - - +
82G MET* 1.3 51.3 + - - +
84G LYS* 3.4 0.5 - - - +
85G ILE* 3.1 15.2 + - - +
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Residues in contact with MET 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G ASN* 3.2 27.4 - - - +
17G CYS* 4.7 0.2 - - - -
69G TYR* 2.3 2.0 - - - -
70G PRO* 3.8 7.2 - - + +
71G ILE* 3.4 37.2 - - + -
76G VAL* 3.5 24.7 - - + -
78G ASN 3.1 20.3 + - - +
79G TRP* 3.9 7.4 - - + +
80G ASP 3.4 0.2 - - - -
81G ASP* 1.3 73.7 - - - +
83G GLU* 1.3 62.8 + - - +
85G ILE* 2.8 42.9 + - + +
86G TRP* 3.1 50.9 + - + +
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Residues in contact with GLU 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR* 2.9 21.1 - - + +
79G TRP 3.0 21.3 + - - +
80G ASP* 3.3 10.5 - - - +
82G MET* 1.3 74.2 - - - +
84G LYS* 1.3 64.9 + - - +
86G TRP* 3.3 10.3 + - - +
87G HIS* 3.1 21.0 + - - +
118G LYS* 4.5 6.4 + - - -
122G ILE* 3.9 35.6 - - + +
126G THR* 3.9 23.3 + - + +
127G PHE* 4.0 6.5 - - + -
120P LYS* 5.3 7.8 - - - +
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Residues in contact with LYS 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ILE* 2.7 26.6 - - + +
35G VAL* 2.6 19.4 + - - +
67G LEU 2.9 5.2 - - - -
68G LYS* 0.4 255.9 + - + +
69G TYR* 0.8 210.3 - - + +
81G ASP 3.4 0.2 - - - +
83G GLU* 1.3 66.2 - - - +
85G ILE* 1.3 63.6 + - - +
86G TRP 3.2 0.2 + - - -
87G HIS 3.3 0.5 + - - -
88G HIS* 3.0 20.3 + - - +
122P VAL* 3.4 14.6 - - + +
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Residues in contact with ILE 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G CYS* 3.9 16.6 - - - -
31G PHE* 4.0 12.8 - - + -
32G PRO 5.1 2.0 - - - +
33G SER* 4.2 30.1 - - - +
34G ILE* 5.1 12.8 - - + +
69G TYR* 4.8 0.4 - - + -
70G PRO* 3.6 26.5 - - + -
71G ILE* 5.0 0.2 - - + -
81G ASP 3.1 9.6 + - - +
82G MET* 2.8 34.1 + - + +
84G LYS* 1.3 75.1 - - - +
86G TRP* 1.3 61.1 - - + +
88G HIS* 3.2 9.2 + - - +
89G THR* 2.8 31.1 + - - +
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Residues in contact with TRP 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G VAL* 3.7 20.8 - - + +
12G ASN* 2.9 39.2 + - - -
76G VAL* 5.6 1.8 - - + -
79G TRP* 4.1 17.3 - + - -
82G MET* 3.1 47.0 + - + +
83G GLU* 3.8 6.7 - - - +
85G ILE* 1.3 76.9 - - + +
87G HIS* 1.3 63.7 + - - +
89G THR* 2.8 28.2 + - - -
90G PHE* 3.1 13.8 + + + -
105G LEU* 4.4 10.5 - - + -
119G MET* 4.2 26.5 - - + -
122G ILE* 4.1 20.6 - - + -
123G MET* 3.5 27.1 - - + -
127G PHE* 3.9 12.3 - + + -
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Residues in contact with HIS 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR 4.6 2.7 + - - +
83G GLU 3.1 13.0 + - - +
84G LYS* 3.4 9.6 - - - +
86G TRP* 1.3 72.5 - - - +
88G HIS* 1.3 57.9 + - - +
90G PHE* 4.5 0.4 - - - -
91G TYR* 2.9 76.9 + + + +
92G ASN* 5.4 2.9 - - - -
127G PHE* 3.7 18.3 - - + -
118P GLY 5.6 1.3 - - - -
119P VAL* 4.4 8.5 - - + -
120P LYS* 4.0 44.7 + - + +
122P VAL* 4.2 8.1 - - + -
143P THR* 4.1 18.6 - - + +
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Residues in contact with HIS 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G PHE* 4.2 22.0 - + - +
84G LYS 3.0 12.8 + - - +
85G ILE* 3.3 9.2 - - - +
87G HIS* 1.3 73.6 - - - +
89G THR* 1.3 58.5 + - - +
92G ASN* 3.0 43.5 + - + +
93G GLU* 2.7 65.1 + - - +
122P VAL* 4.3 18.8 + - + +
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Residues in contact with THR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G VAL* 3.9 22.7 - - + +
17G CYS* 5.7 0.3 - - - -
19G ALA* 3.7 29.8 - - + -
31G PHE* 3.5 18.5 - - + -
85G ILE* 2.8 18.3 + - - +
86G TRP* 2.8 26.5 + - - -
88G HIS* 1.3 72.6 - - - +
90G PHE* 1.3 57.2 + - + +
93G GLU* 3.3 8.8 + - + +
94G LEU* 2.7 41.9 + - + +
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Residues in contact with PHE 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 3.3 34.8 - - + -
10G VAL* 4.5 17.7 - - + -
86G TRP* 3.1 30.6 + + + -
87G HIS* 4.1 2.2 - - - +
89G THR* 1.3 77.9 - - + +
91G TYR* 1.3 60.5 + - + +
94G LEU* 4.8 1.3 - - + -
95G ARG 2.8 30.8 + - - -
96G VAL* 2.8 23.0 + - + +
98G PRO* 3.6 33.0 - - + -
103G VAL* 4.0 17.5 - - + -
105G LEU* 5.6 0.2 - - + -
123G MET* 4.0 30.1 - - + -
127G PHE* 4.2 18.4 - + + -
142P TRP* 3.6 0.7 - - - -
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Residues in contact with TYR 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G HIS* 2.9 72.3 + + + +
90G PHE* 1.3 64.7 - - + +
92G ASN* 1.3 64.4 + - - +
96G VAL 4.0 0.7 - - - -
98G PRO* 3.7 23.2 - - + +
99G GLU* 4.8 3.8 + - - -
127G PHE* 4.1 21.2 + + - -
142P TRP* 1.2 59.0 - - + +
143P THR* 4.5 6.5 - - + +
146P LEU* 1.0 128.5 - - + +
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Residues in contact with ASN 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G HIS* 5.4 2.5 - - - -
88G HIS* 3.0 44.5 + - + +
91G TYR* 1.3 95.2 + - - +
93G GLU* 1.3 71.4 + - - +
94G LEU 3.9 0.2 - - - -
95G ARG* 3.5 18.1 - - - +
43P TRP* 4.6 5.0 - - - -
47P GLN* 4.3 4.2 + - - +
122P VAL* 5.0 5.5 - - - +
124P ILE* 4.2 14.7 - - - +
139P GLY* 2.7 45.2 + - - -
142P TRP* 3.7 0.7 - - - -
143P THR* 3.3 10.0 + - - -
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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
------------------------------------------------------------
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