Contacts of the helix formed by residues 112 - 128 (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 PRO 112 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197F GLY* 6.5 1.8 - - - -
73G HIS* 3.9 13.2 - - + -
75G ILE* 3.8 16.6 - - + -
110G LEU 3.6 1.3 - - - +
111G ASN* 1.3 96.2 - - - +
113G LYS* 1.3 64.7 + - - +
114G ALA* 3.4 2.2 - - + +
115G ASN* 3.0 33.5 + - - +
116G ARG* 3.3 5.4 + - - +
177G ARG* 2.8 13.9 - - - +
179G ASP* 5.0 5.2 - - - +
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Residues in contact with LYS 113 (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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195F GLU 3.5 9.0 + - - +
196F ARG* 3.1 51.3 - - - +
197F GLY* 5.2 1.5 - - - +
111G ASN 3.5 2.0 + - - -
112G PRO* 1.3 69.6 - - - +
114G ALA* 1.3 63.8 + - + +
116G ARG* 3.2 19.1 + - - +
117G GLU* 3.2 18.6 + - - +
177G ARG* 4.8 0.4 - - - +
371G HIS* 3.5 34.7 - - + +
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Residues in contact with ALA 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G PRO* 3.4 1.5 - - + +
113G LYS* 1.3 77.0 - - + +
115G ASN* 1.3 65.4 + - - +
117G GLU* 3.7 12.2 - - - +
118G LYS* 2.8 28.9 + - - +
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Residues in contact with ASN 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ILE* 3.3 28.3 - - - +
76G VAL* 3.5 18.6 + - + +
79G TRP* 4.1 22.1 - - + +
111G ASN* 3.2 23.9 + - - +
112G PRO* 3.0 22.7 + - - +
114G ALA* 1.3 78.0 + - - +
116G ARG* 1.3 65.5 + - - +
118G LYS* 3.0 2.8 + - - +
119G MET* 2.9 29.1 + - + +
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Residues in contact with ARG 116 (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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107G GLU* 3.0 51.4 + - - +
111G ASN* 3.5 24.2 - - - +
112G PRO 3.8 3.6 - - - +
113G LYS* 3.2 12.0 + - - +
115G ASN* 1.3 75.1 - - - +
117G GLU* 1.3 61.8 + - - +
119G MET* 3.4 13.7 + - + +
120G THR* 2.9 28.0 + - - -
134G VAL* 4.4 8.5 + - + +
370G VAL* 3.2 34.9 + - + +
371G HIS* 3.8 21.7 + - + +
374G CYS* 3.0 36.8 + - - +
375G PHE* 5.4 0.2 - - - +
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Residues in contact with GLU 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G LYS* 3.2 15.8 + - - +
114G ALA* 3.8 11.4 - - - +
115G ASN 3.2 0.2 - - - -
116G ARG* 1.3 74.2 - - - +
118G LYS* 1.3 66.2 + - - +
120G THR* 2.9 3.7 + - - -
121G GLN* 2.9 25.8 + - - +
367G PRO* 3.9 30.3 - - + +
368G SER* 4.2 14.0 + - - -
370G VAL* 4.0 7.6 - - - -
371G HIS* 2.8 31.0 + - + +
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Residues in contact with LYS 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G TRP* 3.4 52.4 - - + +
80G ASP* 5.8 0.6 + - - -
83G GLU* 4.5 6.5 + - - -
114G ALA 2.8 22.2 + - - +
115G ASN* 3.0 3.3 + - - +
117G GLU* 1.3 71.4 - - - +
119G MET* 1.3 57.7 + - - +
121G GLN* 3.1 16.1 - - + +
122G ILE* 3.0 50.5 + - + +
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Residues in contact with MET 119 (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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12G ASN* 5.7 0.7 - - - -
76G VAL* 6.4 1.3 - - + -
79G TRP* 4.2 14.5 - - + -
86G TRP* 4.2 22.4 - - + -
105G LEU* 3.5 28.5 - - + -
106G THR 4.7 5.2 - - - +
107G GLU* 4.4 7.9 - - + -
111G ASN* 3.5 28.3 - - - +
115G ASN* 2.9 18.6 + - + +
116G ARG* 3.5 10.8 - - - +
118G LYS* 1.3 75.3 - - - +
120G THR* 1.4 61.2 + - - +
122G ILE* 4.4 4.0 - - - +
123G MET* 3.2 30.7 + - - +
132G MET* 3.9 1.0 - - + +
134G VAL* 3.9 24.2 - - + -
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Residues in contact with THR 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ARG 2.9 15.1 + - - -
117G GLU 2.9 8.4 + - - -
119G MET* 1.4 74.1 - - - +
121G GLN* 1.3 59.8 + - - +
123G MET* 3.6 0.7 + - - +
124G PHE* 2.9 50.7 + - + -
132G MET* 4.1 15.1 - - - -
357G ILE* 5.3 1.8 - - + -
362G TYR* 3.7 25.8 - - + -
367G PRO* 4.2 11.0 - - + +
369G ILE* 4.9 6.5 - - + -
370G VAL* 3.0 28.2 - - + +
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Residues in contact with GLN 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G GLU* 2.9 12.6 + - - +
118G LYS* 3.1 25.7 - - + +
120G THR* 1.3 76.0 - - - +
122G ILE* 1.4 56.3 + - + +
124G PHE* 3.7 0.3 - - - +
125G GLU* 2.9 71.0 + - - +
362G TYR* 3.3 17.4 + - - -
367G PRO* 3.9 19.9 - - + +
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Residues in contact with ILE 122 (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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79G TRP* 3.5 35.9 - - + -
83G GLU* 3.9 30.7 - - + +
86G TRP* 4.1 16.2 - - + -
118G LYS* 3.0 34.5 + - + +
119G MET* 4.4 3.1 - - - +
121G GLN* 1.4 74.6 - - + +
123G MET* 1.3 70.7 + - - +
126G THR* 2.8 38.1 + - - +
127G PHE* 2.9 32.4 + - + -
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Residues in contact with MET 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G TRP* 3.5 42.4 - - + -
90G PHE* 4.0 17.0 - - + -
103G VAL* 3.8 22.7 - - - -
105G LEU* 3.8 14.6 - - + -
119G MET 3.2 20.0 + - - +
120G THR 3.9 2.2 - - - +
122G ILE* 1.3 82.1 - - + +
124G PHE* 1.3 57.9 + - - +
127G PHE* 3.1 37.8 + - + +
128G ASN 3.2 3.5 + - - -
129G THR* 2.7 26.6 + - - +
132G MET* 3.8 26.0 - - + -
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Residues in contact with PHE 124 (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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120G THR* 2.9 36.0 + - + +
123G MET* 1.3 76.7 - - - +
125G GLU* 1.3 59.5 + - - +
128G ASN* 3.0 26.7 - - - +
129G THR* 3.0 32.8 - - - +
131G ALA* 4.0 6.3 - - - -
132G MET* 3.6 24.9 - - + -
357G ILE* 3.6 28.9 - - + -
358G SER 4.0 6.3 - - - -
359G LYS* 3.7 36.0 + - + +
362G TYR* 3.3 44.0 - + + -
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Residues in contact with GLU 125 (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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121G GLN* 2.9 41.0 + - - +
124G PHE* 1.3 71.8 - - - +
126G THR* 1.3 67.2 + - - +
128G ASN* 4.3 4.7 + - - +
359G LYS* 4.7 6.5 - - - +
362G TYR* 2.8 31.9 + - + +
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Residues in contact with THR 126 (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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83G GLU* 3.9 22.6 + - - +
122G ILE* 2.8 35.7 + - + +
125G GLU* 1.3 77.4 - - - +
127G PHE* 1.3 78.2 + - + -
128G ASN* 5.3 0.4 - - - +
120P LYS* 6.5 0.4 - - - -
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Residues in contact with PHE 127 (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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69G TYR 5.8 0.2 - - - -
83G GLU* 4.0 10.8 - - + -
86G TRP* 3.9 16.8 - + + -
87G HIS* 3.7 40.8 - - + -
90G PHE* 4.2 8.5 - + + -
91G TYR* 4.1 24.1 + + - -
98G PRO* 3.3 31.8 - - + +
99G GLU* 3.8 6.2 - - - +
122G ILE* 2.9 33.8 + - + -
123G MET* 3.4 26.2 - - + +
126G THR* 1.3 90.4 - - + +
128G ASN* 1.3 72.7 + - - +
129G THR* 3.4 5.6 - - - +
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Residues in contact with ASN 128 (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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99G GLU* 3.1 37.2 + - + +
123G MET 3.2 0.4 + - - -
124G PHE 3.0 19.5 + - - +
125G GLU 4.3 4.2 - - - +
126G THR 3.6 1.6 - - - -
127G PHE* 1.3 80.8 - - - +
129G THR* 1.3 62.3 + - - +
359G LYS* 3.8 20.4 + - - +
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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
------------------------------------------------------------
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