Contacts of the helix formed by residues 93 - 111 (chain h) in PDB entry 3J9X
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 GLY 93 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92h SER* 1.3 77.6 - - - +
94h PRO* 1.3 68.3 - - - -
95h ALA 3.3 1.6 - - - -
96h LEU* 2.8 28.6 + - - +
97h VAL* 3.2 17.0 + - - +
133h VAL* 4.5 9.9 - - - -
64j THR* 4.5 0.7 - - - -
65j GLN* 5.3 2.2 - - - -
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Residues in contact with PRO 94 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93h GLY* 1.3 83.5 - - - -
95h ALA* 1.3 63.1 + - - +
97h VAL* 3.0 6.4 + - - +
98h ASN* 2.9 25.4 + - - +
133h VAL* 3.8 25.7 - - + -
64j THR* 3.3 16.6 - - + +
65j GLN* 3.4 39.3 - - - +
66j TYR 4.7 0.7 - - - -
67j GLY* 3.9 10.5 - - - -
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Residues in contact with ALA 95 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90h ILE* 3.6 22.6 - - + +
93h GLY 3.1 0.6 + - - -
94h PRO* 1.3 79.9 - - - +
96h LEU* 1.3 57.0 + - - +
98h ASN* 3.3 2.2 + - - +
99h MET* 3.0 24.9 + - - +
64j THR* 3.2 18.8 + - - +
67j GLY* 3.5 16.3 - - - -
68j ILE 3.6 21.5 - - - +
69j THR* 3.4 14.3 - - + +
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Residues in contact with LEU 96 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83h VAL* 4.5 3.4 - - + +
86h ALA* 3.8 32.8 - - + +
87h LEU* 3.6 40.6 - - + +
90h ILE* 4.0 4.9 - - + +
91h GLY 3.4 12.5 + - - +
92h SER* 3.8 11.0 - - - -
93h GLY 2.8 16.7 + - - +
95h ALA* 1.3 72.2 - - - +
97h VAL* 1.3 63.5 + - + +
99h MET* 3.1 6.2 + - + +
100h ILE* 2.8 50.8 + - + +
126h THR* 4.8 10.3 - - + -
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Residues in contact with VAL 97 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93h GLY* 3.2 8.7 + - - +
94h PRO 3.0 8.2 + - - +
96h LEU* 1.3 80.4 - - + +
98h ASN* 1.3 66.0 + - - +
100h ILE* 3.2 5.3 + - + -
101h ASN* 2.9 29.0 + - - +
130h THR* 3.5 20.6 + - - +
131h GLY 3.7 26.7 - - - +
132h TYR* 4.2 7.0 - - - +
133h VAL* 3.8 33.9 - - + +
134h SER 5.2 1.1 - - - +
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Residues in contact with ASN 98 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109g SER 3.5 22.3 - - - +
110g ALA* 3.6 4.0 - - - +
112g ASN* 5.1 10.0 - - - +
94h PRO* 2.9 12.8 + - - +
95h ALA* 3.4 8.1 - - - +
97h VAL* 1.3 80.4 - - - +
99h MET* 1.3 64.6 + - - +
101h ASN* 3.5 9.6 + - - +
102h GLY 3.3 13.3 + - - -
67j GLY* 3.1 35.0 + - - -
69j THR* 4.4 7.6 - - + -
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Residues in contact with MET 99 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437 A 4.1 12.6 - - - +
106g TYR* 4.6 12.6 - - - +
110g ALA* 3.9 20.6 + - - +
111g PHE* 3.7 31.4 - - + -
82h LYS* 5.9 2.2 - - - -
86h ALA* 3.8 23.8 - - + -
90h ILE* 3.8 22.2 - - + -
95h ALA 3.0 13.8 + - - +
96h LEU* 3.3 12.6 - - + +
98h ASN* 1.3 76.3 - - - +
100h ILE* 1.3 60.1 + - + +
102h GLY* 3.2 3.3 + - - -
103h LEU* 2.9 33.7 + - + +
69j THR* 4.7 5.6 - - + -
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Residues in contact with ILE 100 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79h PHE* 5.1 0.9 - - + -
83h VAL* 4.3 22.7 - - + -
86h ALA* 6.0 0.2 - - + -
96h LEU* 2.8 48.1 + - + +
97h VAL* 3.8 3.6 - - + +
99h MET* 1.3 74.7 - - + +
101h ASN* 1.3 58.7 + - - +
103h LEU* 4.1 6.5 - - + -
104h LYS* 2.7 33.4 + - + +
122h VAL* 4.3 19.7 - - + -
126h THR* 4.1 24.5 - - + -
130h THR* 3.6 34.8 - - + +
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Residues in contact with ASN 101 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109g SER* 4.2 8.6 + - - +
97h VAL* 2.9 22.8 + - - +
98h ASN* 3.7 9.9 + - - +
100h ILE* 1.3 76.0 - - - +
102h GLY* 1.3 62.2 + - - +
104h LYS* 3.6 3.4 + - - +
105h GLY* 3.2 19.4 + - - -
130h THR* 2.5 31.6 + - - +
131h GLY* 2.9 34.0 + - - -
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Residues in contact with GLY 102 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105g GLY 4.2 2.2 - - - -
106g TYR* 3.7 11.4 + - - -
109g SER* 2.9 25.4 + - - -
110g ALA* 4.1 10.8 - - - -
98h ASN 3.3 4.2 + - - -
99h MET 3.2 5.8 + - - -
101h ASN* 1.3 76.7 - - - +
103h LEU* 1.3 60.6 + - - +
105h GLY* 3.4 1.3 + - - -
106h TYR* 2.9 30.3 + - - +
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Residues in contact with LEU 103 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106g TYR* 4.0 11.5 - - + -
79h PHE* 3.7 10.1 - - + -
82h LYS* 3.5 51.4 - - + +
83h VAL* 3.7 33.9 - - + +
99h MET* 2.9 24.9 + - + +
100h ILE* 3.6 8.1 - - + +
102h GLY* 1.3 74.3 - - - +
104h LYS* 1.3 66.9 + - - +
106h TYR* 3.2 9.9 - - + +
107h TYR* 3.0 38.1 + - + -
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Residues in contact with LYS 104 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79h PHE* 3.8 18.1 - - + -
100h ILE* 2.7 23.9 + - + +
101h ASN* 3.8 3.8 - - - +
103h LEU* 1.3 73.2 - - - +
105h GLY* 1.3 63.9 + - - +
107h TYR* 3.1 4.9 + - - +
108h ILE* 3.0 45.9 + - + +
115h PRO* 4.4 12.8 - - - +
118h LEU* 4.0 14.0 - - + +
119h ASP* 2.7 39.9 + - - +
122h VAL* 6.0 1.3 - - + -
130h THR* 4.3 19.6 - - + +
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Residues in contact with GLY 105 (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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102g GLY 5.0 0.9 - - - -
105g GLY* 5.9 3.6 - - - -
106g TYR 5.7 0.2 - - - -
101h ASN 3.2 11.9 + - - -
102h GLY* 3.8 2.7 - - - -
104h LYS* 1.3 77.7 - - - +
106h TYR* 1.3 62.7 + - - +
108h ILE* 3.2 12.3 + - - +
109h SER* 3.0 29.4 + - - -
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Residues in contact with TYR 106 (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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1968 T 4.2 0.2 + - - -
1978 A 3.3 16.0 + - - -
82g LYS* 2.7 34.1 + - - -
99g MET* 4.7 3.8 - - - -
102g GLY 3.5 27.3 + - - -
103g LEU* 4.1 15.0 - - + -
106g TYR* 3.7 25.7 - + + +
82h LYS* 5.0 6.1 - - + -
102h GLY 2.9 19.0 + - - +
103h LEU* 3.2 13.2 - - + +
105h GLY* 1.3 74.5 - - - +
107h TYR* 1.3 79.8 + + - +
109h SER* 3.7 0.5 + - - -
110h ALA* 2.8 44.6 + - + +
111h PHE* 3.7 29.6 - + - -
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Residues in contact with TYR 107 (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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1968 T 4.4 6.9 - - + +
1978 A 3.4 24.7 + - - -
71e PRO* 6.5 1.1 - - + -
75h ILE* 3.5 38.4 - - + -
78h GLY* 3.5 4.9 - - - -
79h PHE* 3.5 40.9 + + + -
82h LYS* 4.6 4.7 - - + -
103h LEU* 3.0 29.8 + - + +
104h LYS 3.8 5.8 - - - +
106h TYR* 1.3 95.2 - + - +
108h ILE* 1.3 67.5 + - - +
111h PHE* 3.0 46.5 + + - +
113h ALA* 3.1 22.0 + - + +
118h LEU* 4.4 2.7 - - + -
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Residues in contact with ILE 108 (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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104h LYS* 3.0 46.4 + - + +
105h GLY* 3.2 11.4 + - - +
107h TYR* 1.3 76.8 - - - +
109h SER* 1.3 62.6 + - - +
112h ASN* 3.0 25.5 - - - +
113h ALA 3.4 16.1 + - - +
115h PRO* 3.9 24.0 - - + -
118h LEU* 3.3 16.4 - - + -
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Residues in contact with SER 109 (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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98g ASN* 3.5 18.4 - - - +
101g ASN* 4.2 7.5 + - - +
102g GLY* 3.0 28.1 + - - -
105h GLY 3.0 11.9 + - - -
108h ILE* 1.3 81.6 - - - +
110h ALA* 1.3 64.7 + - - +
111h PHE 3.4 0.2 - - - -
112h ASN* 4.0 10.5 - - - +
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Residues in contact with ALA 110 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69e THR* 2.6 33.6 + - - +
98g ASN* 3.7 14.1 - - - +
99g MET* 4.2 14.9 - - - +
102g GLY* 4.1 11.4 - - - -
106h TYR* 2.8 35.6 + - + +
109h SER* 1.3 76.1 + - - +
111h PHE* 1.3 70.8 + - + +
112h ASN* 3.6 1.1 + - - +
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Residues in contact with PHE 111 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1968 T 3.6 38.6 - - - -
69e THR* 3.4 17.7 - - - +
70e GLY* 3.6 18.8 - - - -
71e PRO* 4.6 3.1 - - + -
72e ASN* 3.2 18.9 + - - +
99g MET* 3.8 24.0 - - + -
75h ILE* 4.6 13.5 - - + +
106h TYR* 3.7 37.7 - + - -
107h TYR* 3.0 44.4 + + + +
110h ALA* 1.3 80.5 - - + +
112h ASN* 1.3 74.3 + - - +
113h ALA* 3.2 1.7 + - - +
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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