Contacts of the helix formed by residues 93 - 111 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A SER* 1.3 75.1 - - - +
94A PRO* 1.3 68.6 - - - -
95A ALA* 3.3 1.8 - - - -
96A LEU* 2.7 30.2 + - - +
97A VAL* 3.1 15.3 + - - +
133A VAL* 4.3 19.8 - - - +
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Residues in contact with PRO 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 4.6 0.9 - - - +
93A GLY* 1.3 83.6 - - - -
95A ALA* 1.3 64.7 + - - +
97A VAL* 3.0 12.8 + - + +
98A ASN* 2.9 28.9 + - - +
133A VAL* 4.3 8.9 - - + -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 3.5 28.6 - - + +
93A GLY 3.1 1.4 + - - -
94A PRO* 1.3 79.6 - - - +
96A LEU* 1.3 61.9 + - - +
98A ASN* 3.3 12.5 + - - +
99A MET* 3.0 22.9 + - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 4.3 6.3 - - + +
86A ALA* 3.9 28.0 - - + +
87A LEU* 3.8 37.7 - - + +
90A ILE* 4.2 4.7 - - + +
91A GLY 3.6 11.9 + - - +
92A SER* 3.9 11.0 - - - -
93A GLY 2.7 16.7 + - - +
95A ALA* 1.3 70.9 - - - +
97A VAL* 1.3 62.4 + - + +
99A MET* 3.1 5.3 + - + +
100A ILE* 2.8 52.7 + - + +
126A THR* 4.6 13.0 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 3.1 7.4 + - - +
94A PRO* 3.0 9.8 + - + +
96A LEU* 1.3 79.2 - - + +
98A ASN* 1.3 66.7 + - - +
100A ILE* 3.3 0.8 + - + -
101A ASN* 3.1 33.1 + - - +
130A THR* 3.4 25.9 + - - +
131A GLY* 3.6 28.5 - - - +
132A TYR 4.8 2.7 - - - +
133A VAL* 3.7 31.0 - - + -
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Residues in contact with ASN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PRO* 2.9 19.9 + - - +
95A ALA* 3.5 14.0 - - - +
97A VAL* 1.3 82.3 - - - +
99A MET* 1.3 63.5 + - - +
101A ASN* 3.5 8.8 + - - +
102A GLY 3.3 15.2 + - - -
109B SER 3.5 22.7 - - - +
110B ALA* 3.7 8.2 - - - +
112B ASN* 5.2 11.6 + - - +
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48 T 4.1 11.4 - - - +
82A LYS* 4.7 13.0 - - - +
83A VAL* 6.3 0.7 - - - -
86A ALA* 3.8 24.2 - - + -
90A ILE* 3.7 23.3 - - + -
95A ALA 3.0 13.4 + - - +
96A LEU* 3.1 14.3 + - + +
98A ASN* 1.3 77.2 - - - +
100A ILE* 1.3 60.4 + - + +
102A GLY* 3.2 2.9 + - - -
103A LEU* 2.8 32.3 + - + +
106B TYR* 4.7 9.2 - - - -
110B ALA* 4.2 22.7 + - - +
111B PHE* 3.8 29.2 - - + -
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 5.0 3.8 - - + -
83A VAL* 4.3 19.1 - - + -
96A LEU* 2.8 46.8 + - + +
97A VAL* 3.9 3.8 - - + +
99A MET* 1.3 73.9 - - + +
101A ASN* 1.3 57.7 + - - +
103A LEU* 3.5 7.1 - - + +
104A LYS* 2.8 43.5 + - + +
122A VAL* 4.2 15.5 - - + -
126A THR* 4.1 22.4 - - + -
130A THR* 3.5 34.3 - - + +
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 3.1 33.8 + - - +
98A ASN* 3.7 9.2 + - - +
100A ILE* 1.3 79.1 - - - +
102A GLY* 1.3 60.7 - - - +
104A LYS* 3.5 8.2 + - - +
105A GLY* 3.2 17.8 + - - -
130A THR* 3.3 20.9 - - - +
131A GLY* 4.3 7.1 + - - -
109B SER* 4.2 8.2 + - - +
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Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASN 3.3 4.4 + - - -
99A MET 3.2 6.2 + - - -
101A ASN* 1.3 76.6 - - - +
103A LEU* 1.3 60.9 + - - +
105A GLY* 3.1 3.9 + - - -
106A TYR 2.9 23.6 + - - -
105B GLY 5.3 0.2 - - - -
106B TYR* 3.5 19.7 - - - -
109B SER* 3.0 24.6 + - - -
110B ALA* 4.0 9.4 - - - -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.6 17.3 - - + -
82A LYS* 3.5 46.4 - - + +
83A VAL* 3.6 31.4 - - + +
99A MET* 2.8 23.1 + - + +
100A ILE* 3.5 8.5 - - + +
102A GLY* 1.3 73.0 - - - +
104A LYS* 1.3 64.5 + - - +
106A TYR* 3.1 11.7 + - + +
107A TYR* 3.0 40.8 + - + -
106B TYR* 3.9 10.8 - - + -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.8 28.3 - - + -
100A ILE* 2.8 34.5 + - + +
101A ASN* 3.7 7.3 + - - +
103A LEU* 1.3 72.4 - - - +
105A GLY* 1.3 58.7 - - - +
107A TYR* 3.2 1.6 + - - +
108A ILE* 2.8 54.6 + - + +
115A PRO* 5.0 4.9 - - - +
118A LEU* 4.8 6.1 - - + -
119A ASP* 2.7 37.3 + - - +
122A VAL* 5.0 2.0 - - + -
129A PRO* 6.1 0.2 - - - +
130A THR* 4.6 12.4 - - + +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN 3.2 8.0 + - - -
102A GLY* 3.1 8.9 + - - -
104A LYS* 1.3 77.4 - - - +
106A TYR* 1.3 58.0 + - - +
108A ILE* 4.5 6.3 - - - +
109A SER* 2.6 35.9 + - - -
102B GLY 4.4 3.4 - - - -
105B GLY* 5.9 2.7 - - - -
106B TYR 5.3 1.8 - - - -
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3357 A 3.8 5.0 + - - -
3367 T 2.9 18.9 + - - -
82A LYS* 5.6 3.1 - - - -
102A GLY 2.9 11.9 + - - +
103A LEU* 3.2 15.9 - - + +
105A GLY* 1.3 74.6 - - - +
107A TYR* 1.3 85.6 + + - +
110A ALA* 2.8 41.6 + - + +
111A PHE* 3.7 26.4 - + - -
82B LYS* 2.8 39.1 + - - -
99B MET* 4.6 7.2 - - - +
102B GLY 3.7 15.8 + - - -
103B LEU* 4.0 12.8 - - + -
106B TYR* 3.7 31.6 - + + -
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3357 A 4.5 4.9 - - + +
3367 T 3.3 35.6 + - - -
75A ILE* 3.5 37.7 - - + -
78A GLY* 3.5 9.8 - - - -
79A PHE* 3.7 30.7 - + + -
82A LYS* 5.2 1.3 - - + -
103A LEU* 3.0 25.9 + - + +
104A LYS 4.0 1.6 - - - +
106A TYR* 1.3 99.2 - + - +
108A ILE* 1.3 66.9 + - - +
111A PHE* 3.1 40.6 + + + -
113A ALA* 3.0 26.1 + - + +
118A LEU* 4.4 7.2 - - + -
71D PRO* 6.5 0.9 - - + -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A LYS* 2.8 45.0 + - + +
105A GLY* 4.1 6.1 - - - +
107A TYR* 1.3 72.2 - - - +
109A SER* 1.3 61.6 + - - +
112A ASN* 3.1 25.8 - - - +
113A ALA 3.6 16.8 - - - +
115A PRO* 3.9 31.9 - - + -
118A LEU* 3.3 21.1 - - + -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY* 2.6 22.0 + - - -
108A ILE* 1.3 83.8 - - - +
110A ALA* 1.3 61.4 + - - +
112A ASN* 4.0 10.4 - - - +
98B ASN* 3.5 17.6 - - - +
101B ASN* 4.2 5.5 + - - +
102B GLY* 2.9 22.5 - - - -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 2.8 26.2 + - + +
109A SER* 1.3 81.0 + - - +
111A PHE* 1.3 61.7 + - + +
112A ASN* 5.1 1.7 + - - -
98B ASN* 3.6 13.4 - - - +
99B MET* 3.9 34.8 + - - +
102B GLY* 4.1 4.9 - - - -
69D THR* 2.6 34.0 + - - +
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3357 A 3.8 23.8 - - - -
75A ILE* 4.8 12.9 - - + +
106A TYR* 3.7 34.1 - + - -
107A TYR* 3.1 46.7 + + + +
110A ALA* 1.3 80.1 - - + +
112A ASN* 1.3 75.3 + - - +
113A ALA* 3.2 2.2 + - - +
99B MET* 3.7 28.0 - - + -
69D THR* 3.4 16.8 - - - +
70D GLY* 3.5 31.4 - - - -
71D PRO* 4.6 3.6 - - + -
72D ASN* 3.3 19.6 + - - +
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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
------------------------------------------------------------
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