Contacts of the helix formed by residues 111 - 131 (chain T) in PDB entry 3J7Y
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 LYS 111 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010 ILE* 3.7 28.5 - - + +
2672A A 3.2 25.6 - - - +
2673A G 3.7 15.0 - - - +
117O ARG* 4.7 4.5 + - - +
82T TYR* 4.2 13.0 - - - +
86T LYS* 5.0 7.4 + - + +
89T TYR* 4.5 13.3 - - - +
90T LEU* 4.4 9.0 - - + -
109T ASN* 2.9 28.8 + - - +
110T ASP* 1.3 81.8 - - - +
112T LYS* 1.3 67.0 + - - +
114T ALA* 3.1 23.4 + - + +
115T LYS* 3.9 11.2 + - - +
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Residues in contact with LYS 112 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2358A A 4.9 12.8 + - - -
2359A C 5.7 4.8 + - - -
2672A A 4.3 1.2 + - - -
2673A G 3.0 37.4 + - - +
2674A U 3.4 20.6 - - - +
81T LYS* 3.1 36.3 - - - +
82T TYR* 3.7 9.0 - - + -
111T LYS* 1.3 71.9 - - - +
113T GLY* 1.3 64.1 + - - +
114T ALA 3.2 0.5 + - - -
115T LYS* 3.4 36.0 + - - +
116T ILE* 3.8 16.8 - - + +
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Residues in contact with GLY 113 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82T TYR* 3.7 12.9 + - - -
87T MET* 3.4 26.4 - - - +
90T LEU* 3.8 5.2 - - - -
111T LYS 3.3 0.4 - - - -
112T LYS* 1.3 78.6 - - - +
114T ALA* 1.3 58.0 + - - +
115T LYS 3.2 0.2 - - - -
116T ILE* 3.2 15.3 + - - +
117T ILE* 3.0 32.4 + - - +
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Residues in contact with ALA 114 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90T LEU* 3.7 29.1 - - + +
106T LEU* 3.8 25.3 - - + +
109T ASN* 3.6 20.6 - - + +
111T LYS* 3.1 14.4 + - + +
113T GLY* 1.3 76.9 - - - +
115T LYS* 1.3 57.7 - - + +
117T ILE* 3.3 3.6 + - - +
118T LYS* 2.9 29.5 + - - +
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Residues in contact with LYS 115 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O SER* 4.7 10.3 + - - -
117O ARG* 3.3 31.9 - - - +
106T LEU 5.8 0.2 - - - -
111T LYS 4.4 8.3 - - - +
112T LYS* 3.4 25.7 + - + +
114T ALA* 1.3 76.5 - - + +
116T ILE* 1.3 58.9 + - + +
118T LYS* 3.2 13.5 + - - +
119T GLU* 2.7 47.1 + - - +
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Residues in contact with ILE 116 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77T ARG* 3.9 26.0 - - - +
80T ILE* 3.4 51.6 - - + -
81T LYS 5.3 0.2 - - - +
82T TYR* 5.6 1.1 - - + -
87T MET* 5.2 1.1 - - + -
112T LYS* 3.8 31.2 - - + +
113T GLY* 3.2 15.8 + - - +
115T LYS* 1.3 82.0 - - + +
117T ILE* 1.3 60.3 + - + +
119T GLU* 3.2 11.8 + - - +
120T VAL* 2.9 34.5 + - + +
174T TYR* 5.7 0.2 - - + -
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Residues in contact with ILE 117 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87T MET* 3.5 25.6 - - + -
90T LEU* 3.3 38.6 - - + -
91T ALA 4.5 1.1 - - - +
94T ILE* 3.1 36.8 - - + -
106T LEU* 3.6 6.3 - - + -
113T GLY 3.0 15.1 + - - +
114T ALA* 3.7 5.8 - - - +
116T ILE* 1.3 77.4 - - + +
118T LYS* 1.3 56.3 + - - +
120T VAL* 3.2 3.9 + - - +
121T LEU* 2.9 31.1 + - + +
174T TYR* 3.3 39.9 - - + +
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Residues in contact with LYS 118 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103T LEU* 4.1 21.1 - - + +
106T LEU* 3.5 24.1 - - + +
107T GLU* 3.5 43.3 + - + +
114T ALA 2.9 13.8 + - - +
115T LYS* 3.4 15.3 - - - +
117T ILE* 1.3 76.2 - - - +
119T GLU* 1.3 64.6 + - - +
121T LEU* 3.2 5.4 + - - +
122T LEU* 2.9 53.2 + - + +
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Residues in contact with GLU 119 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77T ARG* 3.6 20.6 + - - +
115T LYS* 2.7 43.2 + - - +
116T ILE* 3.3 11.5 + - - +
118T LYS* 1.3 82.1 + - - +
120T VAL* 1.3 58.7 - - - +
122T LEU* 3.2 16.2 + - + +
123T GLU* 2.9 29.9 + - - +
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Residues in contact with VAL 120 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75T HIS* 3.7 21.1 - - + +
76T CYS 4.4 7.9 - - - +
77T ARG* 3.3 38.4 - - + +
116T ILE* 2.9 22.2 + - + +
117T ILE 3.4 7.9 - - - +
119T GLU* 1.3 76.7 - - - +
121T LEU* 1.3 57.3 + - - +
123T GLU* 3.3 8.2 + - - +
124T ALA* 2.9 27.4 + - + +
174T TYR* 4.1 13.9 - - + -
176T VAL* 3.8 26.5 - - + -
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Residues in contact with LEU 121 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94T ILE* 4.2 4.0 - - + -
99T ILE* 4.7 6.6 - - + +
102T ALA* 4.1 5.8 - - + -
103T LEU* 3.4 25.8 - - + -
106T LEU* 3.5 31.2 - - + -
117T ILE* 2.9 20.6 + - + +
118T LYS 3.5 3.8 - - - +
120T VAL* 1.3 76.4 - - - +
122T LEU* 1.3 58.0 + - - +
124T ALA* 3.2 6.1 + - - +
125T GLN* 2.9 28.6 + - - +
142T ILE* 3.6 38.1 - - + -
174T TYR* 5.3 0.4 - - - +
176T VAL* 4.0 16.8 - - + -
178T LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 122 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103T LEU* 3.7 26.2 - - + -
118T LYS* 2.9 42.1 + - + +
119T GLU* 3.4 15.9 - - + +
121T LEU* 1.3 76.5 - - - +
123T GLU* 1.3 57.4 + - - +
125T GLN* 3.2 14.2 + - - +
126T ASP* 2.9 40.1 + - - +
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Residues in contact with GLU 123 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75T HIS* 2.6 35.5 + - + +
77T ARG* 5.6 4.3 - - - +
119T GLU 2.9 13.2 + - - +
120T VAL* 3.6 9.8 - - - +
122T LEU* 1.3 77.0 - - - +
124T ALA* 1.3 56.8 + - - +
126T ASP* 3.2 12.1 + - + +
127T MET* 2.9 32.7 + - + +
130T ARG* 5.2 3.3 + - - +
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Residues in contact with ALA 124 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T ILE* 4.5 5.4 - - + +
75T HIS* 4.2 21.9 - - + -
120T VAL* 2.9 14.3 + - + +
121T LEU* 3.2 11.0 + - - +
123T GLU* 1.3 75.3 - - - +
125T GLN* 1.3 57.6 + - - +
127T MET* 3.2 11.3 + - - +
128T ALA* 2.9 28.8 + - - +
176T VAL* 5.1 5.2 - - + -
178T LEU* 3.3 27.9 - - + +
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Residues in contact with GLN 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99T ILE* 3.2 30.3 - - + +
100T ASP* 4.0 8.5 + - - -
103T LEU* 4.3 6.5 - - - +
121T LEU 2.9 12.3 + - - +
122T LEU* 3.3 26.1 - - - +
124T ALA* 1.3 74.6 - - - +
126T ASP* 1.3 61.8 + - - +
128T ALA* 3.2 4.7 + - - +
129T VAL* 2.9 31.2 + - - +
137T ARG* 3.5 48.0 + - + +
140T LEU* 3.9 23.6 - - + -
178T LEU* 4.1 0.4 - - - +
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Residues in contact with ASP 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T LEU* 2.9 25.7 + - - +
123T GLU* 3.2 12.5 + - + +
125T GLN* 1.3 81.6 - - - +
127T MET* 1.3 56.7 + - - +
129T VAL* 3.2 6.4 + - - +
130T ARG* 2.9 51.6 + - - +
137T ARG* 5.4 5.2 + - - -
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Residues in contact with MET 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55T ASN* 4.0 14.4 - - - +
73T ILE* 4.7 8.1 - - + -
74T TYR 3.9 9.4 - - - +
75T HIS* 3.5 48.2 - - + +
123T GLU* 2.9 13.9 + - + +
124T ALA* 3.3 11.4 - - - +
126T ASP* 1.3 77.1 - - - +
128T ALA* 1.3 57.8 + - - +
130T ARG* 4.1 18.4 - - - +
131T ASP* 2.8 41.6 + - - +
132T HIS* 3.1 22.6 + - + -
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Residues in contact with ALA 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T ILE* 3.2 33.8 - - + +
124T ALA 2.9 11.4 + - - +
125T GLN 3.3 9.2 - - - +
127T MET* 1.3 75.1 - - - +
129T VAL* 1.3 62.4 + - + +
132T HIS* 3.5 2.4 - - - -
133T ASN 3.2 9.2 + - - -
134T VAL* 2.9 32.2 + - + -
140T LEU* 3.8 22.4 - - + -
178T LEU* 5.2 0.2 - - + -
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Residues in contact with VAL 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125T GLN 2.9 12.7 + - - +
126T ASP* 3.2 8.2 + - - +
128T ALA* 1.3 81.3 - - + +
130T ARG* 1.3 72.6 + - + +
133T ASN* 4.5 3.1 + - - -
134T VAL* 3.5 19.7 + - + +
135T GLU 4.4 8.5 - - - +
136T PHE 5.2 0.2 - - - -
137T ARG* 3.7 37.2 - - + +
140T LEU* 5.8 0.4 - - + -
278d LYS* 4.3 15.7 + - - +
280d VAL* 6.4 1.8 - - + -
281d MET 5.8 4.0 - - - +
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Residues in contact with ARG 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123T GLU* 5.2 3.8 + - - +
126T ASP* 2.9 30.3 + - - +
127T MET* 4.1 26.5 - - - +
129T VAL* 1.3 89.7 - - + +
131T ASP* 1.3 90.1 + - - +
132T HIS 3.6 0.2 - - - -
133T ASN* 4.4 3.7 + - - -
103V ASP* 5.8 2.4 + - - -
278d LYS* 5.8 1.6 + - - -
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Residues in contact with ASP 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127T MET* 2.8 24.6 + - + +
130T ARG* 1.3 108.6 + - - +
132T HIS* 1.3 74.6 + - + +
133T ASN* 3.5 2.4 + - - +
179d LYS* 4.8 13.3 + - - -
227d ARG* 5.5 1.6 - - - -
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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
------------------------------------------------------------
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