Contacts of the helix formed by residues 112 - 128 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197G GLY* 6.5 2.0 - - - -
73H HIS* 3.9 11.7 - - + -
75H ILE* 3.8 17.9 - - + -
110H LEU 3.6 1.6 - - - +
111H ASN* 1.3 97.3 - - - +
113H LYS* 1.3 65.1 + - - +
114H ALA* 3.4 2.2 - - + +
115H ASN* 3.0 33.3 + - - +
116H ARG* 3.3 5.5 + - - +
177H ARG* 2.8 13.7 - - - +
179H ASP* 5.0 5.2 - - - +
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Residues in contact with LYS 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G GLU 3.5 10.0 + - - +
196G ARG* 3.1 50.1 - - - +
197G GLY* 5.2 1.5 - - - +
111H ASN 3.5 2.5 + - - -
112H PRO* 1.3 69.2 - - - +
114H ALA* 1.3 64.7 + - + +
116H ARG* 3.2 19.6 + - - +
117H GLU* 3.2 18.8 + - - +
177H ARG* 4.8 0.4 - - - +
371H HIS* 3.5 33.3 - - + +
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H PRO* 3.4 1.6 - - + +
113H LYS* 1.3 76.5 - - + +
115H ASN* 1.3 63.4 + - - +
117H GLU* 3.8 12.2 - - - +
118H LYS* 2.8 29.8 + - - +
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Residues in contact with ASN 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ILE* 3.3 28.1 - - - +
76H VAL 3.5 18.0 + - - +
79H TRP* 4.1 20.9 - - + +
111H ASN* 3.2 23.2 + - - +
112H PRO* 3.0 23.2 + - - +
114H ALA* 1.3 77.7 + - - +
116H ARG* 1.3 65.6 + - - +
118H LYS* 3.0 3.3 + - - +
119H MET* 2.9 28.3 + - + +
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Residues in contact with ARG 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H GLU* 3.0 52.5 + - - +
111H ASN* 3.5 23.6 - - - +
112H PRO 3.3 4.2 + - - +
113H LYS* 3.2 12.4 + - - +
115H ASN* 1.3 75.9 - - - +
117H GLU* 1.3 61.4 + - - +
119H MET* 3.4 13.2 + - - +
120H THR* 2.9 28.5 + - - -
134H VAL* 4.4 9.1 - - + +
370H VAL* 3.2 34.5 + - + +
371H HIS* 3.8 20.9 + - + +
374H CYS* 3.0 36.8 + - - +
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Residues in contact with GLU 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H LYS* 3.2 17.3 + - - +
114H ALA* 3.8 11.7 - - - +
115H ASN 3.2 0.2 - - - -
116H ARG* 1.3 73.6 - - - +
118H LYS* 1.3 67.0 + - - +
120H THR* 2.9 3.7 + - - -
121H GLN* 2.9 25.2 + - - +
367H PRO* 3.9 29.6 - - + +
368H SER* 4.2 13.5 + - - -
370H VAL* 4.0 7.4 - - - -
371H HIS* 2.8 29.3 + - + +
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Residues in contact with LYS 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H TRP* 3.4 52.4 - - + +
80H ASP* 5.8 0.4 + - - -
83H GLU* 4.5 6.1 + - - -
114H ALA 2.8 22.8 + - - +
115H ASN 3.0 4.0 + - - +
117H GLU* 1.3 69.8 - - - +
119H MET* 1.3 57.6 + - - +
121H GLN* 3.1 16.6 - - + +
122H ILE* 3.0 50.2 + - + +
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Residues in contact with MET 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASN* 5.7 0.4 - - - -
76H VAL* 6.4 1.6 - - + -
79H TRP* 4.2 13.8 - - + -
86H TRP* 4.2 22.4 - - + -
105H LEU* 3.5 27.8 - - + -
106H THR 4.7 5.2 - - - +
107H GLU* 4.4 7.9 - - + -
111H ASN* 3.5 28.5 - - - +
115H ASN* 2.9 19.5 + - + +
116H ARG* 3.5 11.0 - - - +
118H LYS* 1.3 76.0 - - - +
120H THR* 1.4 59.6 + - - +
122H ILE* 4.4 4.0 - - - +
123H MET* 3.2 31.2 + - - +
132H MET* 3.9 0.6 - - - +
134H VAL* 3.9 24.2 - - + -
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Residues in contact with THR 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H ARG 2.9 14.8 + - - -
117H GLU 2.9 7.3 + - - -
119H MET* 1.4 73.6 - - - +
121H GLN* 1.3 59.2 + - - +
123H MET* 3.6 0.7 + - - +
124H PHE* 2.9 50.5 + - + -
132H MET* 4.1 15.1 - - - -
357H ILE* 5.3 2.2 - - + -
362H TYR* 3.7 26.2 - - + -
367H PRO* 4.2 11.4 - - + +
369H ILE* 4.9 6.3 - - + -
370H VAL* 3.0 28.1 - - + +
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Residues in contact with GLN 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H GLU* 2.9 12.4 + - - +
118H LYS* 3.1 26.3 - - + +
120H THR* 1.3 75.8 - - - +
122H ILE* 1.4 58.2 + - + +
124H PHE* 3.7 0.3 - - - +
125H GLU* 2.9 71.3 + - - +
362H TYR* 3.3 16.5 + - - -
367H PRO* 3.9 20.5 - - + +
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Residues in contact with ILE 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H TRP* 3.5 35.7 - - + -
83H GLU* 3.9 29.6 - - + +
86H TRP* 4.1 16.8 - - + -
118H LYS* 3.0 35.3 + - + +
119H MET* 4.4 3.4 - - - +
121H GLN* 1.4 74.6 - - + +
123H MET* 1.3 71.3 + - - +
126H THR* 2.8 38.9 + - - +
127H PHE* 2.9 30.7 + - + -
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Residues in contact with MET 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H TRP* 3.5 41.1 - - + -
90H PHE* 4.0 17.5 - - + -
103H VAL* 3.8 23.3 - - - -
105H LEU* 3.8 14.8 - - + -
119H MET 3.2 21.6 + - - +
120H THR 3.9 1.8 - - - +
122H ILE* 1.3 81.9 - - + +
124H PHE* 1.3 56.8 + - - +
127H PHE* 3.1 37.6 + - + +
128H ASN 3.2 3.6 + - - -
129H THR* 2.7 27.0 + - - +
132H MET* 3.8 25.6 - - + -
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Residues in contact with PHE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H THR* 2.9 35.1 + - + +
121H GLN 3.9 0.2 - - - +
123H MET* 1.3 76.6 - - - +
125H GLU* 1.3 58.5 + - - +
128H ASN* 3.0 26.3 - - - +
129H THR* 3.0 32.5 - - - +
131H ALA* 4.0 6.5 - - - -
132H MET* 3.6 23.8 - - + -
357H ILE* 3.6 29.2 - - + -
358H SER 4.0 6.7 - - - -
359H LYS* 3.7 36.9 + - + +
362H TYR* 3.3 44.9 - + + -
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H GLN* 2.9 42.6 + - - +
124H PHE* 1.3 72.0 - - - +
126H THR* 1.3 66.5 + - - +
128H ASN* 4.4 4.9 + - - +
359H LYS* 4.7 6.7 - - - +
362H TYR* 2.8 30.8 + - + +
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Residues in contact with THR 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H GLU* 3.9 23.3 + - - +
122H ILE* 2.8 35.2 + - + +
125H GLU* 1.3 77.3 - - - +
127H PHE* 1.3 78.7 + - + +
128H ASN* 5.3 0.4 - - - +
120S LYS* 6.5 1.1 - - - -
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Residues in contact with PHE 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H TYR 5.8 0.2 - - - -
83H GLU* 4.0 11.4 - - + -
86H TRP* 3.9 16.6 - - + -
87H HIS* 3.7 40.8 - - + -
90H PHE* 4.2 7.4 - + + -
91H TYR* 4.1 24.1 + + - -
98H PRO* 3.3 31.0 - - + +
99H GLU* 3.8 6.4 - - - +
122H ILE* 2.9 34.2 + - + -
123H MET* 3.4 26.7 - - + +
126H THR* 1.3 89.7 - - + +
128H ASN* 1.3 73.1 + - - +
129H THR* 3.4 5.4 - - - +
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Residues in contact with ASN 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H GLU* 3.1 37.6 + - + +
123H MET 3.2 0.8 + - - -
124H PHE 3.0 19.7 + - - +
125H GLU 4.3 4.0 - - - +
126H THR 3.6 1.2 - - - +
127H PHE* 1.3 81.4 - - - +
129H THR* 1.3 62.6 + - - +
359H LYS* 3.8 20.9 + - - +
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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