Contacts of the helix formed by residues 100 - 118 (chain f) 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 MET 100 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99f ASP* 1.3 81.2 - - - +
101f THR* 1.3 76.4 + - + +
103f ALA* 3.2 6.8 + - - +
104f GLU* 2.9 50.2 + - + +
153f HIS* 3.5 65.8 + - + +
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Residues in contact with THR 101 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99f ASP 4.2 9.5 + - - -
100f MET* 1.3 91.2 - - + +
102f LEU* 1.3 67.4 + - - +
104f GLU* 3.2 16.7 + - - +
105f SER* 2.9 29.0 + - - -
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Residues in contact with LEU 102 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99f ASP* 3.2 25.2 + - - +
101f THR* 1.3 87.0 + - - +
103f ALA* 1.3 57.4 + - - +
105f SER* 3.2 9.9 + - - -
106f TYR* 2.9 28.3 + - - +
181f GLY* 6.1 2.2 - - - +
182f VAL* 4.8 13.9 - - + -
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Residues in contact with ALA 103 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99f ASP 2.9 12.6 + - - +
100f MET* 3.2 12.3 + - - +
102f LEU* 1.3 76.9 - - - +
104f GLU* 1.3 57.0 + - - +
106f TYR* 3.2 9.6 + - - +
107f ALA* 2.9 28.6 + - - +
153f HIS* 4.6 15.0 - - + +
155f ARG* 4.6 13.7 - - + +
182f VAL* 4.8 17.9 - - + +
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Residues in contact with GLU 104 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1633B U 4.6 9.6 + - - -
1634B A 5.3 6.4 + - - -
100f MET* 2.9 34.1 + - + +
101f THR* 3.4 19.1 - - - +
103f ALA* 1.3 76.8 - - - +
105f SER* 1.3 57.1 + - - +
107f ALA* 3.2 4.5 + - - +
108f GLN* 2.9 33.9 + - - +
155f ARG* 3.7 37.2 + - + +
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Residues in contact with SER 105 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101f THR 2.9 12.8 + - - -
102f LEU* 3.4 15.0 - - - -
104f GLU* 1.3 75.9 - - - +
106f TYR* 1.3 58.5 + - - +
108f GLN* 3.2 15.7 + - - +
109f TYR* 2.9 29.0 + - - +
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Residues in contact with TYR 106 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102f LEU 2.9 12.7 + - - +
103f ALA* 3.4 13.2 - - - +
105f SER* 1.3 77.7 - - - +
107f ALA* 1.3 58.4 + - - +
109f TYR* 3.2 17.7 + + + +
110f VAL* 2.9 53.2 + - + +
174f ILE* 2.4 42.4 + - - +
176f SER 6.0 1.8 - - - -
182f VAL* 6.0 6.5 - - + -
183f ARG 5.0 4.0 - - - -
184f LEU* 3.6 26.1 - - + +
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Residues in contact with ALA 107 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634B A 5.6 0.4 - - - -
103f ALA 2.9 12.5 + - - +
104f GLU 3.2 9.8 + - - +
106f TYR* 1.3 79.7 - - - +
108f GLN* 1.3 55.8 + - - +
110f VAL* 3.2 10.0 + - - +
111f HIS* 2.9 29.6 + - - +
155f ARG* 4.0 36.8 - - + +
157f VAL* 4.0 18.1 - - + +
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Residues in contact with GLN 108 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1632B U 3.0 24.7 + - - +
1634B A 3.2 43.0 + - - +
1635B C 4.0 10.1 + - - +
104f GLU* 2.9 16.0 + - - +
105f SER* 3.2 16.7 + - - +
107f ALA* 1.3 74.9 - - - +
109f TYR* 1.3 57.7 + - - +
111f HIS* 3.2 9.1 + - - +
112f ASN* 2.9 38.6 + - - +
155f ARG* 5.8 0.4 - - - +
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Residues in contact with TYR 109 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818 LYS* 5.3 12.3 - - - -
858 ARG* 2.7 45.4 + - - -
888 GLU* 4.7 6.8 + - - -
105f SER 2.9 13.4 + - - +
106f TYR* 3.3 22.0 - + + +
108f GLN* 1.3 76.3 - - - +
110f VAL* 1.3 65.6 + - + +
112f ASN* 3.2 11.8 + - + +
113f LEU* 2.9 48.8 + - + +
173f ILE* 5.1 8.3 - - - +
174f ILE* 6.3 1.3 - - - -
176f SER 6.2 0.8 - - - -
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Residues in contact with VAL 110 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106f TYR* 2.9 48.6 + - + +
107f ALA* 3.4 10.1 - - - +
109f TYR* 1.3 83.8 - - + +
111f HIS* 1.3 57.0 + - - +
113f LEU* 3.2 8.4 + - - +
114f CYS* 2.9 27.4 + - - +
157f VAL* 4.2 25.1 - - + -
159f ILE* 5.0 1.6 - - + -
170f PHE* 4.5 8.7 - - + -
174f ILE* 4.1 31.2 - - + -
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Residues in contact with HIS 111 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1634B A 3.3 33.6 + - + +
1635B C 3.6 42.7 + - - -
107f ALA 2.9 13.4 + - - +
108f GLN 3.3 10.8 - - - +
110f VAL* 1.3 77.7 - - - +
112f ASN* 1.3 56.6 + - - +
114f CYS* 3.2 7.4 + - - +
115f ASN* 2.9 34.1 + - - -
121f VAL* 3.2 41.0 - - + +
123f GLU 6.0 0.2 - - - -
124f SER* 5.1 11.1 + - - -
157f VAL* 4.7 10.3 - - + -
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Residues in contact with ASN 112 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1627B C 6.1 1.6 - - - +
1628B C 5.6 5.3 + - - -
1635B C 4.1 31.1 + - - +
1636B A 4.6 5.4 + - - -
108f GLN* 2.9 24.3 + - - +
109f TYR* 3.4 12.2 - - + +
111f HIS* 1.3 75.7 - - - +
113f LEU* 1.3 58.7 + - - +
115f ASN* 3.2 9.7 + - - +
116f SER* 2.9 29.0 + - - -
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Residues in contact with LEU 113 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858 ARG* 5.2 6.5 - - - +
928 ILE* 4.7 7.0 - - + -
109f TYR* 2.9 40.1 + - + +
110f VAL* 3.4 11.2 - - - +
112f ASN* 1.3 75.5 - - - +
114f CYS* 1.3 58.4 + - - +
116f SER* 3.2 10.6 + - - -
117f LEU* 2.9 59.2 + - + +
170f PHE* 4.7 7.0 - - + -
173f ILE* 3.5 46.9 - - + -
174f ILE* 5.2 3.6 - - + +
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Residues in contact with CYS 114 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110f VAL 2.9 12.6 + - - +
111f HIS* 3.2 10.5 + - - +
113f LEU* 1.3 77.3 - - - +
115f ASN* 1.3 63.3 + - - +
117f LEU* 3.2 2.6 + - - -
118f SER 3.0 18.4 + - - -
119f ILE* 3.2 50.3 + - - +
121f VAL* 3.4 26.9 - - + -
157f VAL* 5.5 0.4 - - + -
159f ILE* 3.6 29.6 - - + -
170f PHE* 4.2 6.9 - - + -
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Residues in contact with ASN 115 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635B C 2.9 38.9 + - - -
1636B A 3.6 10.8 + - - +
111f HIS* 2.9 33.6 + - - +
112f ASN* 3.2 13.0 + - - +
114f CYS* 1.3 76.2 - - - +
116f SER* 1.3 63.6 + - - +
118f SER* 3.3 13.2 + - - -
119f ILE 4.8 4.7 - - - +
121f VAL* 3.9 8.5 - - - +
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Residues in contact with SER 116 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898 ARG* 4.4 24.0 + - - +
112f ASN 2.9 12.3 + - - -
113f LEU* 3.4 16.8 - - - -
115f ASN* 1.3 78.2 - - - +
117f LEU* 1.3 64.2 + - - +
118f SER* 3.2 7.5 + - - -
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Residues in contact with LEU 117 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928 ILE* 4.2 35.0 - - + -
113f LEU* 2.9 42.4 + - + +
114f CYS 3.2 3.5 + - - +
116f SER* 1.3 76.5 - - - +
118f SER* 1.3 71.5 + - - +
119f ILE* 3.7 3.6 - - + -
166f PHE* 3.5 42.3 - - + -
169f ILE* 5.4 4.7 - - + -
170f PHE* 4.2 22.0 - - + -
173f ILE* 4.9 4.9 - - + -
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Residues in contact with SER 118 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476 ARG 6.2 0.2 - - - -
114f CYS 3.0 3.6 + - - -
115f ASN 3.3 7.6 + - - -
116f SER 3.2 10.0 + - - -
117f LEU* 1.3 83.4 - - - +
119f ILE* 1.3 62.0 + - - +
166f PHE* 4.9 2.9 - - - -
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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
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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