Contacts of the helix formed by residues 93 - 111 (chain k) 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 k).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64i THR* 4.6 0.7 - - - -
92k SER* 1.3 77.1 + - - +
94k PRO* 1.3 68.0 - - - -
95k ALA 3.3 1.8 - - - -
96k LEU* 2.7 28.9 + - - +
97k VAL* 3.1 15.1 + - - +
133k VAL* 4.3 19.4 - - - +
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Residues in contact with PRO 94 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64i THR* 3.3 18.2 - - + +
65i GLN* 3.4 27.4 - - + +
66i TYR 4.6 0.2 - - - -
67i GLY* 3.8 10.3 - - - +
92k SER 4.6 0.7 - - - +
93k GLY* 1.3 83.0 - - - -
95k ALA* 1.3 62.7 + - - +
97k VAL* 3.0 13.1 + - + +
98k ASN* 2.9 26.1 + - - +
133k VAL* 4.3 9.5 - - + -
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Residues in contact with ALA 95 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64i THR* 3.3 18.4 + - + +
67i GLY* 3.5 15.5 - - - -
68i ILE 3.7 20.4 - - - +
69i THR* 3.4 14.8 - - + +
90k ILE* 3.5 25.1 - - + -
93k GLY 3.1 0.6 + - - -
94k PRO* 1.3 78.7 - - - +
96k LEU* 1.3 61.5 + - - +
98k ASN* 3.3 1.9 + - - +
99k MET* 3.0 19.6 + - - +
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Residues in contact with LEU 96 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83k VAL* 4.3 6.1 - - + +
86k ALA* 3.9 28.5 - - + +
87k LEU* 3.8 37.9 - - + +
90k ILE* 4.2 5.1 - - + +
91k GLY 3.6 12.1 + - - +
92k SER* 3.9 10.3 - - - -
93k GLY 2.7 16.7 + - - +
95k ALA* 1.3 70.8 - - - +
97k VAL* 1.3 62.1 + - + +
99k MET* 3.1 5.1 + - + +
100k ILE* 2.8 52.5 + - + +
126k THR* 4.6 12.8 - - + -
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Residues in contact with VAL 97 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93k GLY 3.8 6.7 - - - +
94k PRO* 3.0 10.0 + - + +
96k LEU* 1.3 79.1 - - + +
98k ASN* 1.3 66.7 + - - +
100k ILE* 3.3 0.6 + - + -
101k ASN* 3.1 32.7 + - - +
130k THR* 3.4 25.5 + - - +
131k GLY* 3.6 29.2 - - - +
132k TYR 4.8 2.7 - - - +
133k VAL* 3.7 31.4 - - + -
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Residues in contact with ASN 98 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67i GLY* 3.1 35.2 + - - -
69i THR* 4.4 8.3 - - + -
94k PRO* 2.9 12.3 + - - +
95k ALA* 3.5 8.1 - - - +
97k VAL* 1.3 81.6 - - - +
99k MET* 1.3 62.2 + - - +
101k ASN* 3.5 9.0 + - - +
102k GLY 3.3 15.8 + - - -
109l SER 3.5 22.7 - - - +
110l ALA* 3.7 2.7 - - - +
112l ASN* 5.2 8.4 + - - +
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Residues in contact with MET 99 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208 T 4.1 11.7 - - - +
69i THR* 4.6 6.1 - - + -
82k LYS* 4.7 12.3 - - - +
83k VAL* 6.3 0.7 - - - -
86k ALA* 3.8 23.8 - - + -
90k ILE* 3.7 23.1 - - + -
95k ALA 3.0 12.6 + - - +
96k LEU* 3.1 13.9 + - + +
98k ASN* 1.3 76.5 - - - +
100k ILE* 1.3 59.9 + - + +
102k GLY* 3.2 3.3 + - - -
103k LEU* 2.8 32.2 + - + +
106l TYR* 4.7 10.3 - - - -
110l ALA* 4.2 20.4 + - - +
111l PHE* 3.8 28.3 - - + -
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Residues in contact with ILE 100 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79k PHE* 5.0 3.4 - - + -
83k VAL* 4.3 19.3 - - + -
96k LEU* 2.8 46.5 + - + +
97k VAL* 3.9 3.8 - - + +
99k MET* 1.3 74.3 - - + +
101k ASN* 1.3 57.8 + - - +
103k LEU* 3.2 6.9 + - + +
104k LYS* 2.8 43.2 + - + +
122k VAL* 4.2 15.9 - - + -
126k THR* 4.1 22.7 - - + -
130k THR* 3.5 34.8 - - + +
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Residues in contact with ASN 101 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97k VAL* 3.1 34.9 + - - +
98k ASN* 3.7 9.5 + - - +
100k ILE* 1.3 76.8 - - - +
102k GLY* 1.3 61.2 + - - +
104k LYS* 3.5 8.4 + - - +
105k GLY* 3.2 17.3 + - - -
130k THR* 3.3 20.7 - - - +
131k GLY* 4.3 6.9 + - - -
109l SER* 4.2 8.2 + - - +
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Residues in contact with GLY 102 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98k ASN 3.3 4.4 + - - -
99k MET 3.2 6.5 + - - -
101k ASN* 1.3 76.2 - - - +
103k LEU* 1.3 60.2 + - - +
105k GLY* 3.1 4.3 + - - -
106k TYR 2.9 23.6 + - - -
105l GLY 5.3 0.2 - - - -
106l TYR* 3.5 19.4 - - - -
109l SER* 3.0 24.1 + - - -
110l ALA* 4.0 10.3 - - - -
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Residues in contact with LEU 103 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79k PHE* 3.6 17.7 - - + -
82k LYS* 3.5 47.8 - - + +
83k VAL* 3.6 30.5 - - + +
99k MET* 2.8 22.0 + - + +
100k ILE* 3.5 9.0 - - + +
102k GLY* 1.3 72.6 - - - +
104k LYS* 1.3 65.9 + - - +
106k TYR* 3.1 11.5 + - + +
107k TYR* 3.0 40.5 + - + -
106l TYR* 3.9 10.1 - - + -
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Residues in contact with LYS 104 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79k PHE* 3.8 28.0 - - + -
100k ILE* 2.8 35.2 + - + +
101k ASN* 3.7 7.5 + - - +
103k LEU* 1.3 72.6 - - - +
105k GLY* 1.3 59.6 + - - +
107k TYR* 3.2 1.4 + - - +
108k ILE* 2.8 54.0 + - + +
115k PRO* 5.0 5.5 - - - +
118k LEU* 4.8 6.5 - - + -
119k ASP* 2.7 37.9 + - - +
122k VAL* 5.0 1.8 - - + -
129k PRO* 6.1 0.4 - - - +
130k THR* 4.6 12.4 - - + +
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Residues in contact with GLY 105 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101k ASN 3.2 8.9 + - - -
102k GLY* 3.1 8.1 + - - -
104k LYS* 1.3 78.1 - - - +
106k TYR* 1.3 57.9 + - - +
108k ILE* 4.6 6.5 - - - -
109k SER* 2.6 36.5 + - - -
102l GLY 4.4 3.6 - - - -
105l GLY* 5.9 2.2 - - - -
106l TYR 5.3 2.0 - - - -
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Residues in contact with TYR 106 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197 A 3.8 5.5 + - - -
1207 T 2.9 18.4 + - - -
82k LYS* 5.6 4.0 - - - -
102k GLY 2.9 12.1 + - - +
103k LEU* 3.2 15.5 - - + +
105k GLY* 1.3 73.9 - - - +
107k TYR* 1.3 85.2 + + - +
110k ALA* 2.8 41.3 + - + +
111k PHE* 3.7 26.1 - + - -
82l LYS* 2.8 39.9 + - - -
99l MET* 4.6 7.4 - - - +
102l GLY 3.7 15.8 + - - -
103l LEU* 4.0 14.1 - - + -
106l TYR* 3.7 31.2 - + + -
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Residues in contact with TYR 107 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197 A 4.5 5.0 - - + +
1207 T 3.3 35.0 + - - -
75k ILE* 3.5 37.0 - - + -
78k GLY* 3.5 10.0 - - - -
79k PHE* 3.7 29.2 - + + -
82k LYS* 5.2 0.9 - - + -
103k LEU* 3.0 25.4 + - + +
104k LYS 4.0 1.8 - - - +
106k TYR* 1.3 99.4 - + - +
108k ILE* 1.3 67.9 + - - +
111k PHE* 3.1 40.6 + + + -
113k ALA* 3.0 26.1 + - + +
118k LEU* 4.4 7.9 - - + -
71n PRO* 6.5 0.7 - - + -
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Residues in contact with ILE 108 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104k LYS* 2.8 45.6 + - + +
105k GLY* 4.1 5.2 - - - +
107k TYR* 1.3 73.1 - - - +
109k SER* 1.3 62.1 + - - +
112k ASN* 3.1 24.9 - - - +
113k ALA 3.6 15.3 - - - +
115k PRO* 3.9 30.7 - - + -
118k LEU* 3.3 21.8 - - + -
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Residues in contact with SER 109 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105k GLY* 2.6 21.8 + - - -
108k ILE* 1.3 83.8 - - - +
110k ALA* 1.3 60.8 + - - +
111k PHE 3.5 0.2 - - - -
112k ASN* 4.0 11.0 - - - +
98l ASN* 3.5 17.4 - - - +
101l ASN* 4.2 6.0 + - - +
102l GLY* 2.9 22.2 - - - -
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Residues in contact with ALA 110 (chain k).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106k TYR* 2.8 26.5 + - + +
109k SER* 1.3 79.5 + - - +
111k PHE* 1.3 61.7 + - + +
112k ASN* 3.6 1.9 + - - -
98l ASN* 3.6 13.1 - - - +
99l MET* 3.9 35.7 + - - +
102l GLY* 4.1 4.7 - - - -
69n THR* 2.6 34.0 + - - +
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Residues in contact with PHE 111 (chain k).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197 A 3.8 24.7 - - - -
75k ILE* 4.8 13.1 - - + +
106k TYR* 3.7 35.0 - + - -
107k TYR* 3.1 46.2 + + + +
110k ALA* 1.3 79.3 - - + +
112k ASN* 1.3 74.1 + - - +
113k ALA* 3.2 2.6 + - - +
99l MET* 3.7 27.1 - - + -
69n THR* 3.4 17.0 - - - +
70n GLY* 3.5 31.6 - - - -
71n PRO* 4.6 3.8 - - + -
72n ASN* 3.3 19.4 + - - +
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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