Contacts of the helix formed by residues 112 - 128 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197H GLY* 6.5 1.3 - - - -
73I HIS* 3.9 12.1 - - + -
75I ILE* 3.8 18.6 - - + -
110I LEU 3.6 1.8 - - - +
111I ASN* 1.3 96.9 - - - +
113I LYS* 1.3 64.3 + - - +
114I ALA* 3.4 2.5 - - + +
115I ASN* 3.0 32.0 + - - +
116I ARG* 3.3 5.9 + - - +
177I ARG* 3.3 13.9 - - - +
179I ASP* 5.0 4.7 - - - +
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Residues in contact with LYS 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H GLU 3.5 8.9 + - - +
196H ARG* 3.1 51.0 - - - +
197H GLY* 5.2 1.3 - - - +
111I ASN 3.5 2.7 + - - -
112I PRO* 1.3 69.4 - - - +
114I ALA* 1.3 63.2 + - + +
116I ARG* 3.2 20.3 + - - +
117I GLU* 3.2 19.3 + - - +
177I ARG* 4.8 0.2 - - - +
371I HIS* 3.5 33.2 - - + +
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Residues in contact with ALA 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I PRO* 3.4 2.1 - - + +
113I LYS* 1.3 77.2 - - + +
115I ASN* 1.3 63.1 + - - +
117I GLU* 3.7 11.1 - - - +
118I LYS* 2.8 29.3 + - - +
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Residues in contact with ASN 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I ILE* 3.3 28.5 - - - +
76I VAL* 3.5 18.8 + - - +
79I TRP* 4.1 20.3 - - + +
111I ASN* 3.2 24.0 + - - +
112I PRO* 3.0 23.9 + - - +
114I ALA* 1.3 78.4 + - - +
116I ARG* 1.3 65.5 + - - +
118I LYS* 3.0 2.8 + - - +
119I MET* 2.9 28.4 + - + +
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Residues in contact with ARG 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I GLU* 3.0 53.1 + - - +
111I ASN* 3.5 23.8 - - - +
112I PRO 3.3 4.0 + - - +
113I LYS* 3.2 12.6 + - - +
115I ASN* 1.3 74.7 - - - +
117I GLU* 1.3 61.9 + - - +
119I MET* 3.4 13.5 + - + +
120I THR* 2.9 28.3 + - - -
134I VAL* 4.4 9.0 + - + +
370I VAL* 3.2 35.0 + - + +
371I HIS* 3.8 21.3 + - + +
374I CYS* 3.0 37.2 + - - +
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Residues in contact with GLU 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LYS* 3.2 16.4 + - - +
114I ALA* 3.8 11.9 - - - +
115I ASN 3.2 0.4 - - - -
116I ARG* 1.3 74.2 - - - +
118I LYS* 1.3 66.6 + - - +
120I THR* 2.9 3.7 + - - -
121I GLN* 2.9 25.6 + - - +
367I PRO* 3.9 29.2 - - + +
368I SER* 4.2 14.3 + - - -
370I VAL* 4.0 7.4 - - - -
371I HIS* 2.8 30.5 + - + -
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Residues in contact with LYS 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I TRP* 3.4 55.3 - - + +
80I ASP* 5.7 0.6 + - - -
83I GLU* 4.5 5.7 + - - -
114I ALA 2.8 22.8 + - - +
115I ASN 3.0 4.2 + - - +
117I GLU* 1.3 69.8 - - - +
119I MET* 1.3 57.0 + - - +
121I GLN* 3.1 16.6 - - + +
122I ILE* 3.0 51.3 + - + +
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Residues in contact with MET 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I ASN* 5.7 0.7 - - - -
76I VAL* 6.4 1.6 - - + -
79I TRP* 4.2 13.6 - - + -
86I TRP* 4.2 21.8 - - + -
105I LEU* 3.5 27.8 - - + -
106I THR 4.7 5.4 - - - +
107I GLU* 4.4 7.9 - - + -
111I ASN* 3.5 29.2 - - - +
115I ASN* 2.9 19.0 + - + +
116I ARG* 3.5 11.2 - - - +
118I LYS* 1.3 76.2 - - - +
120I THR* 1.4 60.6 + - - +
122I ILE* 4.6 3.4 - - - +
123I MET* 3.2 30.8 + - - +
132I MET* 3.9 0.6 - - - +
134I VAL* 3.9 25.4 - - + -
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Residues in contact with THR 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I ARG 2.9 14.8 + - - -
117I GLU 2.9 7.7 + - - -
119I MET* 1.4 74.5 - - - +
121I GLN* 1.3 59.8 + - - +
123I MET* 3.6 1.0 + - - +
124I PHE* 2.9 49.9 + - + +
132I MET* 4.1 14.8 - - - -
357I ILE* 5.3 2.0 - - + -
362I TYR* 3.7 25.6 - - + -
367I PRO* 4.2 10.8 - - + +
369I ILE* 4.9 6.5 - - + -
370I VAL* 3.0 28.0 - - + +
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Residues in contact with GLN 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I GLU* 2.9 12.9 + - - +
118I LYS* 3.1 25.5 - - + +
120I THR* 1.3 77.5 - - - +
122I ILE* 1.4 58.2 + - + +
124I PHE* 3.7 0.3 - - - +
125I GLU* 2.9 69.5 + - - +
362I TYR* 3.3 17.0 + - - -
367I PRO* 3.9 20.3 - - + +
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Residues in contact with ILE 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I TRP* 3.5 35.7 - - + -
83I GLU* 3.9 31.0 - - + +
86I TRP* 4.0 16.4 - - + -
118I LYS* 3.0 34.3 + - + +
119I MET* 4.4 3.1 - - - +
121I GLN* 1.4 75.0 - - + +
123I MET* 1.3 70.7 + - - +
126I THR* 2.8 39.5 + - - +
127I PHE* 2.9 31.6 + - + -
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Residues in contact with MET 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I TRP* 3.5 41.1 - - + -
90I PHE* 4.0 16.4 - - + -
103I VAL* 3.8 22.0 - - - -
105I LEU* 3.8 16.2 - - + -
119I MET 3.2 20.9 + - - +
120I THR 3.9 1.8 - - - +
122I ILE* 1.3 83.1 - - + +
124I PHE* 1.3 56.9 + - - +
127I PHE* 3.1 38.5 + - + +
128I ASN 3.2 3.5 + - - -
129I THR* 2.7 26.1 + - - +
132I MET* 3.8 25.6 - - + -
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Residues in contact with PHE 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I THR* 2.9 35.3 + - + +
123I MET* 1.3 77.3 - - - +
125I GLU* 1.3 59.0 + - - +
128I ASN* 3.0 26.3 - - - +
129I THR* 3.0 33.7 - - - +
131I ALA* 4.0 6.1 - - - -
132I MET* 3.6 23.3 - - + -
357I ILE* 3.6 28.9 - - + -
358I SER 4.0 6.7 - - - -
359I LYS* 3.7 36.3 + - + +
362I TYR* 3.3 45.1 - + + -
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Residues in contact with GLU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I GLN* 2.9 42.9 + - + +
124I PHE* 1.3 72.3 - - - +
126I THR* 1.4 65.3 + - - +
128I ASN* 4.4 4.5 + - - +
359I LYS* 4.7 6.7 - - - +
362I TYR* 2.8 31.4 + - + +
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Residues in contact with THR 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I GLU* 3.9 23.5 + - - +
122I ILE* 2.8 34.3 + - + +
125I GLU* 1.4 77.0 - - - +
127I PHE* 1.3 78.4 + - + +
128I ASN* 5.4 0.2 - - - +
120R LYS* 6.5 0.9 - - - -
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Residues in contact with PHE 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I TYR 5.8 0.2 - - - -
83I GLU* 4.0 11.2 - - + -
86I TRP* 3.9 16.4 - + + -
87I HIS* 3.7 41.7 - - + -
90I PHE* 4.2 8.1 - + + -
91I TYR* 4.1 25.2 + + - -
98I PRO* 3.3 32.0 - - + +
99I GLU* 3.8 6.6 - - - +
122I ILE* 2.9 34.2 + - + -
123I MET* 3.4 26.7 - - + +
126I THR* 1.3 89.8 - - + +
128I ASN* 1.3 73.3 + - - +
129I THR* 3.4 5.4 - - - +
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Residues in contact with ASN 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I GLU* 3.1 37.7 + - + +
123I MET 3.2 0.8 + - - -
124I PHE 3.0 19.5 + - - +
125I GLU 5.0 3.8 - - - +
126I THR 3.6 1.4 - - - -
127I PHE* 1.3 81.7 - - - +
129I THR* 1.3 62.5 + - - +
359I LYS* 3.8 20.6 + - - +
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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