Contacts of the helix formed by residues 93 - 111 (chain s) 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 s).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64q THR 4.6 0.4 - - - -
92s SER* 1.3 76.2 - - - +
94s PRO* 1.3 67.8 - - - -
95s ALA 3.3 1.8 - - - -
96s LEU* 2.7 30.7 + - - +
97s VAL* 3.1 15.1 + - - +
133s VAL* 4.3 19.5 - - - +
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Residues in contact with PRO 94 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64q THR* 3.3 17.3 - - + +
65q GLN* 3.4 27.8 - - + +
66q TYR 4.6 0.7 - - - -
67q GLY* 3.8 11.0 - - - +
92s SER 4.6 0.9 - - - +
93s GLY* 1.3 84.5 - - - -
95s ALA* 1.3 63.0 + - - +
97s VAL* 3.0 12.6 + - + +
98s ASN* 2.9 25.2 + - - +
133s VAL* 4.3 8.7 - - + -
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Residues in contact with ALA 95 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64q THR* 3.3 19.0 + - + +
67q GLY* 3.5 15.7 - - - -
68q ILE 3.7 20.6 - - - +
69q THR* 3.4 14.8 - - + +
90s ILE* 3.5 24.9 - - + +
93s GLY 3.1 0.6 + - - -
94s PRO* 1.3 79.8 - - - +
96s LEU* 1.3 63.1 + - - +
98s ASN* 3.3 1.5 + - - +
99s MET* 3.0 19.1 + - - +
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Residues in contact with LEU 96 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83s VAL* 4.3 6.3 - - + +
86s ALA* 3.9 28.9 - - + +
87s LEU* 3.8 37.7 - - + +
90s ILE* 4.2 5.7 - - + +
91s GLY 3.6 11.9 + - - +
92s SER* 3.9 10.1 - - - -
93s GLY 2.7 16.3 + - - +
95s ALA* 1.3 71.8 - - - +
97s VAL* 1.3 62.8 + - + +
99s MET* 3.1 5.0 + - + +
100s ILE* 2.8 52.4 + - + +
126s THR* 4.6 13.0 - - + -
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Residues in contact with VAL 97 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93s GLY 3.8 7.2 - - - +
94s PRO* 3.0 10.5 + - + +
96s LEU* 1.3 78.7 - - + +
98s ASN* 1.3 66.6 + - - +
100s ILE* 3.3 1.1 + - + +
101s ASN* 3.1 33.1 + - - +
130s THR* 3.4 25.6 + - - +
131s GLY* 3.5 29.8 - - - +
132s TYR 4.8 2.5 - - - +
133s VAL* 3.7 29.6 - - + -
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Residues in contact with ASN 98 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67q GLY* 3.1 35.2 + - - -
69q THR* 4.4 7.6 - - + -
94s PRO* 2.9 12.7 + - - +
95s ALA* 3.5 8.3 - - - +
96s LEU 3.2 0.2 - - - -
97s VAL* 1.3 80.2 - - - +
99s MET* 1.3 62.4 + - - +
101s ASN* 3.5 8.7 + - - +
102s GLY 3.3 15.6 + - - -
109t SER 3.5 22.1 - - - +
110t ALA* 3.7 3.6 - - - +
112t ASN* 5.2 9.3 - - - +
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Residues in contact with MET 99 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2688 T 4.1 11.4 - - - +
69q THR* 4.6 5.8 - - + -
82s LYS* 4.7 12.6 - - - +
83s VAL* 6.3 0.4 - - - -
86s ALA* 3.8 24.7 - - + -
90s ILE* 3.7 22.7 - - + -
95s ALA 3.0 13.7 + - - +
96s LEU* 3.1 13.9 + - + +
98s ASN* 1.3 76.9 - - - +
100s ILE* 1.3 60.2 + - + +
102s GLY* 3.2 3.5 + - - -
103s LEU* 2.8 32.3 + - + +
106t TYR* 4.7 9.9 - - - -
110t ALA* 4.2 20.4 + - - +
111t PHE* 3.8 28.9 - - + -
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Residues in contact with ILE 100 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79s PHE* 5.0 3.6 - - + -
83s VAL* 4.3 18.6 - - + -
96s LEU* 2.8 46.4 + - + +
97s VAL* 3.3 3.8 + - + +
99s MET* 1.3 73.6 - - + +
101s ASN* 1.3 58.0 + - - +
103s LEU* 4.0 6.3 - - + -
104s LYS* 2.8 43.4 + - + +
122s VAL* 4.2 16.2 - - + -
126s THR* 4.1 22.7 - - + -
130s THR* 3.5 35.2 - - + +
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Residues in contact with ASN 101 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97s VAL* 3.1 33.1 + - - +
98s ASN* 3.7 10.3 + - - +
99s MET 3.2 0.2 - - - -
100s ILE* 1.3 78.2 - - - +
102s GLY* 1.3 61.9 + - - +
104s LYS* 3.5 8.0 + - - +
105s GLY* 3.2 17.3 + - - -
130s THR* 3.3 21.2 - - - +
131s GLY* 4.3 7.1 + - - -
109t SER* 4.2 8.9 + - - +
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Residues in contact with GLY 102 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98s ASN 3.3 4.6 + - - -
99s MET 3.2 6.1 + - - -
101s ASN* 1.3 77.0 - - - +
103s LEU* 1.3 59.8 + - - +
105s GLY* 3.1 3.8 + - - -
106s TYR 2.9 23.7 + - - -
106t TYR* 3.5 20.3 - - - -
109t SER* 3.0 23.9 + - - -
110t ALA* 4.0 10.1 - - - -
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Residues in contact with LEU 103 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79s PHE* 3.6 17.9 - - + -
82s LYS* 3.5 46.4 - - + +
83s VAL* 3.6 30.7 - - + +
99s MET* 2.8 22.9 + - + +
100s ILE* 3.5 8.5 - - + +
102s GLY* 1.3 73.8 - - - +
104s LYS* 1.3 64.9 + - - +
106s TYR* 3.1 11.3 + - + +
107s TYR* 3.0 40.7 + - + -
106t TYR* 3.9 9.5 - - + -
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Residues in contact with LYS 104 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79s PHE* 3.8 28.3 - - + -
100s ILE* 2.8 36.0 + - + +
101s ASN* 3.7 7.3 + - - +
103s LEU* 1.3 71.8 - - - +
105s GLY* 1.3 58.7 + - - +
107s TYR* 3.2 1.2 + - - +
108s ILE* 2.8 53.8 + - + +
115s PRO* 5.0 5.7 - - - +
118s LEU* 4.8 7.0 - - + -
119s ASP* 2.7 36.2 + - - +
122s VAL* 5.0 2.2 - - + -
129s PRO* 6.1 0.2 - - - +
130s THR* 4.6 13.1 - - + +
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Residues in contact with GLY 105 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101s ASN 3.2 8.3 + - - -
102s GLY* 3.1 8.2 + - - -
104s LYS* 1.3 77.7 - - - +
106s TYR* 1.3 57.4 + - - +
108s ILE* 4.5 6.3 - - - +
109s SER* 2.6 37.1 + - - -
102t GLY 4.4 3.6 - - - -
105t GLY* 5.9 2.5 - - - -
106t TYR 5.3 2.0 - - - -
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Residues in contact with TYR 106 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717 A 3.8 5.4 + - - -
727 T 2.9 17.9 + - - -
82s LYS* 5.5 4.0 - - - -
102s GLY 2.9 12.1 + - - +
103s LEU* 3.1 16.1 + - + +
105s GLY* 1.3 75.0 - - - +
107s TYR* 1.3 84.2 + + - +
110s ALA* 2.8 42.1 + - + +
111s PHE* 3.7 27.1 - + - -
82t LYS* 2.8 40.3 + - - -
99t MET* 4.6 8.0 - - - +
102t GLY 3.7 15.3 + - - -
103t LEU* 4.0 12.6 - - + -
106t TYR* 3.7 30.7 - + + -
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Residues in contact with TYR 107 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717 A 4.5 5.6 - - + +
727 T 3.3 33.7 + - - -
75s ILE* 3.5 39.0 - - + -
78s GLY* 3.5 10.0 - - - -
79s PHE* 3.7 30.1 - + + -
82s LYS* 5.2 1.6 - - + -
103s LEU* 3.0 25.9 + - + +
104s LYS 4.0 1.8 - - - +
106s TYR* 1.3 96.9 - + - +
108s ILE* 1.3 65.9 + - - +
111s PHE* 3.1 40.4 + + + -
113s ALA* 3.0 26.1 + - + +
118s LEU* 4.4 8.1 - - + -
71v PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104s LYS* 2.8 43.2 + - + +
105s GLY* 4.1 5.2 - - - +
107s TYR* 1.3 72.9 - - - +
109s SER* 1.3 63.0 + - - +
112s ASN* 3.1 24.6 - - - +
113s ALA* 3.6 16.4 + - - +
115s PRO* 3.9 32.1 - - + -
118s LEU* 3.3 21.5 - - + -
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Residues in contact with SER 109 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105s GLY* 2.6 20.8 + - - -
108s ILE* 1.3 84.8 - - - +
110s ALA* 1.3 60.4 + - - +
111s PHE 3.5 0.2 - - - -
112s ASN* 4.0 10.9 - - - +
98t ASN* 3.5 17.4 - - - +
101t ASN* 4.2 6.1 + - - +
102t GLY* 2.9 21.7 - - - -
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Residues in contact with ALA 110 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106s TYR* 2.8 25.9 + - + +
109s SER* 1.3 80.2 + - - +
111s PHE* 1.3 62.4 + - + +
112s ASN* 3.6 2.1 + - - -
98t ASN* 3.6 12.9 - - - +
99t MET* 3.9 35.2 + - - +
102t GLY* 4.1 4.9 - - - -
69v THR* 2.6 34.3 + - - +
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Residues in contact with PHE 111 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717 A 3.8 24.7 - - - -
75s ILE* 4.8 13.5 - - + +
106s TYR* 3.7 34.5 - + - -
107s TYR* 3.1 47.4 + + + +
110s ALA* 1.3 79.2 - - + +
112s ASN* 1.3 74.7 + - - +
113s ALA* 3.3 1.8 + - - +
99t MET* 3.7 28.7 - - + -
69v THR* 3.4 17.3 - - - +
70v GLY* 3.5 30.7 - - - -
71v PRO* 4.6 4.3 - - + -
72v ASN* 3.3 19.0 + - - +
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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