Contacts of the helix formed by residues 93 - 111 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64W THR* 4.6 0.7 - - - -
92Y SER* 1.3 77.1 + - - +
94Y PRO* 1.3 67.8 - - - -
95Y ALA 3.3 1.8 - - - -
96Y LEU* 2.7 29.8 + - - +
97Y VAL* 3.1 14.9 + - - +
133Y VAL* 4.3 18.7 - - - +
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Residues in contact with PRO 94 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64W THR* 3.3 17.0 - - + +
65W GLN* 3.4 26.7 - - + +
66W TYR 4.6 0.4 - - - -
67W GLY* 3.8 11.4 - - - +
92Y SER 4.6 0.2 - - - +
93Y GLY* 1.3 83.7 - - - -
95Y ALA* 1.3 62.8 + - - +
97Y VAL* 3.0 13.0 + - + +
98Y ASN* 2.9 25.7 + - - +
133Y VAL* 4.3 8.9 - - + -
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Residues in contact with ALA 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64W THR* 3.3 18.6 + - + +
67W GLY* 3.6 15.7 - - - -
68W ILE 3.7 20.6 - - - +
69W THR* 3.4 14.0 - - + +
90Y ILE* 3.5 24.7 - - + -
93Y GLY 3.1 0.4 + - - -
94Y PRO* 1.3 79.3 - - - +
96Y LEU* 1.3 62.4 + - - +
98Y ASN* 3.3 1.5 + - - +
99Y MET* 3.0 19.8 + - - +
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Residues in contact with LEU 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Y VAL* 4.3 5.6 - - + +
86Y ALA* 3.9 28.9 - - + -
87Y LEU* 3.8 37.2 - - + +
90Y ILE* 4.2 4.9 - - + +
91Y GLY 3.6 12.7 + - - +
92Y SER* 3.9 11.0 - - - -
93Y GLY 2.7 16.5 + - - +
95Y ALA* 1.3 71.5 - - - +
97Y VAL* 1.3 62.8 + - + +
99Y MET* 3.1 5.9 + - + +
100Y ILE* 2.8 52.3 + - + +
126Y THR* 4.6 13.2 - - + -
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Residues in contact with VAL 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Y GLY* 3.8 7.6 - - - +
94Y PRO* 3.0 11.3 + - + +
96Y LEU* 1.3 78.9 - - + +
98Y ASN* 1.3 66.2 + - - +
100Y ILE* 3.3 1.0 + - + -
101Y ASN* 3.1 33.1 + - - +
130Y THR* 3.4 25.8 + - - +
131Y GLY* 3.5 29.8 - - - +
132Y TYR 4.8 2.9 - - - +
133Y VAL* 3.7 30.1 - - + -
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Residues in contact with ASN 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67W GLY* 3.1 35.6 + - - -
69W THR* 4.4 7.4 - - + -
94Y PRO* 2.9 13.3 + - - +
95Y ALA* 3.5 7.9 - - - +
97Y VAL* 1.3 81.6 - - - +
99Y MET* 1.3 63.1 + - - +
101Y ASN* 3.5 9.1 + - - +
102Y GLY 3.3 15.8 + - - -
109Z SER 3.5 22.7 - - - +
110Z ALA* 3.7 3.7 - - - +
112Z ASN* 5.2 9.7 + - - +
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Residues in contact with MET 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1488 T 4.1 11.7 - - - +
69W THR* 4.6 5.6 - - + -
70W GLY 5.3 0.2 - - - +
82Y LYS* 4.7 13.0 - - - +
83Y VAL* 6.3 0.9 - - - -
86Y ALA* 3.8 22.9 - - + -
90Y ILE* 3.7 23.3 - - + -
95Y ALA 3.0 13.1 + - - +
96Y LEU* 3.3 13.5 - - + +
98Y ASN* 1.3 77.6 - - - +
100Y ILE* 1.3 59.8 + - + +
102Y GLY* 3.2 3.3 + - - -
103Y LEU* 2.8 31.9 + - + +
106Z TYR* 4.7 9.4 - - - -
110Z ALA* 4.2 20.4 + - - +
111Z PHE* 3.8 29.8 - - + -
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Residues in contact with ILE 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Y PHE* 5.0 3.1 - - + -
83Y VAL* 4.3 19.1 - - + -
96Y LEU* 2.8 46.8 + - + +
97Y VAL* 3.3 4.0 + - + +
99Y MET* 1.3 73.9 - - + +
101Y ASN* 1.3 57.9 + - - +
103Y LEU* 4.0 6.3 - - + -
104Y LYS* 2.8 43.0 + - + +
122Y VAL* 4.2 16.4 - - + -
126Y THR* 4.1 22.4 - - + -
130Y THR* 3.5 33.9 - - + +
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Residues in contact with ASN 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Y VAL* 3.1 34.1 + - - +
98Y ASN* 3.7 9.9 + - - +
100Y ILE* 1.3 78.0 - - - +
102Y GLY* 1.3 61.7 + - - +
104Y LYS* 3.5 8.4 + - - +
105Y GLY* 3.2 17.5 + - - -
130Y THR* 3.3 21.1 - - - +
131Y GLY* 4.3 7.1 + - - -
109Z SER* 4.2 8.7 + - - +
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Residues in contact with GLY 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Y ASN 3.3 4.4 + - - -
99Y MET 3.2 6.0 + - - -
101Y ASN* 1.3 75.5 - - - +
103Y LEU* 1.3 59.7 + - - +
105Y GLY* 3.1 3.7 + - - -
106Y TYR 2.9 23.4 + - - -
105Z GLY 5.0 0.4 - - - -
106Z TYR* 3.5 20.5 - - - -
109Z SER* 3.0 23.9 + - - -
110Z ALA* 4.0 10.1 - - - -
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Residues in contact with LEU 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Y PHE* 3.6 17.0 - - + -
82Y LYS* 3.5 46.9 - - + +
83Y VAL* 3.6 31.4 - - + +
99Y MET* 2.8 22.0 + - + +
100Y ILE* 3.5 8.7 - - + +
102Y GLY* 1.3 73.4 - - - +
104Y LYS* 1.3 64.5 + - - +
106Y TYR* 3.1 11.7 + - + +
107Y TYR* 3.0 41.4 + - + -
106Z TYR* 3.9 10.4 - - + -
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Residues in contact with LYS 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79Y PHE* 3.8 28.7 - - + -
100Y ILE* 2.8 35.4 + - + +
101Y ASN* 3.7 7.5 + - - +
103Y LEU* 1.3 71.9 - - - +
105Y GLY* 1.3 58.8 + - - +
107Y TYR* 3.2 1.6 + - - +
108Y ILE* 2.8 53.9 + - + +
115Y PRO* 5.0 5.3 - - - +
118Y LEU* 4.8 6.1 - - + -
119Y ASP* 2.7 37.3 + - - +
122Y VAL* 5.0 2.2 - - + -
129Y PRO* 6.1 0.6 - - - +
130Y THR* 4.6 12.5 - - + +
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Residues in contact with GLY 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Y ASN 3.2 7.8 + - - -
102Y GLY* 3.1 8.2 + - - -
104Y LYS* 1.3 77.7 - - - +
106Y TYR* 1.3 57.1 + - - +
108Y ILE* 4.6 6.5 - - - -
109Y SER* 2.6 36.9 + - - -
102Z GLY* 4.4 3.6 - - - -
105Z GLY* 5.9 2.9 - - - -
106Z TYR 5.3 2.0 - - - -
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Residues in contact with TYR 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1917 A 3.8 5.8 + - - -
1927 T 2.9 17.5 + - - -
82Y LYS* 5.5 3.8 - - - -
102Y GLY 2.9 12.1 + - - +
103Y LEU* 3.2 15.7 - - + +
105Y GLY* 1.3 75.9 - - - +
107Y TYR* 1.3 84.4 + + - +
110Y ALA* 2.8 41.9 + - + +
111Y PHE* 3.7 26.4 - + - -
82Z LYS* 2.8 40.2 + - - -
99Z MET* 4.6 7.6 - - - +
102Z GLY 3.7 15.3 + - - -
103Z LEU* 4.0 13.7 - - + -
106Z TYR* 3.7 31.6 - + + -
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Residues in contact with TYR 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917 A 4.5 4.9 - - + +
1927 T 3.3 34.7 + - - -
75Y ILE* 3.5 37.9 - - + -
78Y GLY* 3.5 10.0 - - - -
79Y PHE* 3.7 30.1 - + + -
82Y LYS* 5.2 1.1 - - + -
103Y LEU* 3.0 26.7 + - + +
104Y LYS 4.0 1.6 - - - +
106Y TYR* 1.3 98.1 - + - +
108Y ILE* 1.3 66.5 + - - +
111Y PHE* 3.1 39.9 + + + -
113Y ALA* 3.0 26.1 + - + +
118Y LEU* 4.4 8.5 - - + -
71b PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Y LYS* 2.8 44.7 + - + +
105Y GLY* 4.1 5.2 - - - +
107Y TYR* 1.3 71.9 - - - +
109Y SER* 1.3 61.5 + - - +
112Y ASN* 3.1 25.1 - - - +
113Y ALA 3.6 16.6 - - - +
115Y PRO* 3.9 30.5 - - + -
118Y LEU* 3.3 21.5 - - + -
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Residues in contact with SER 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Y GLY 2.6 21.4 + - - -
108Y ILE* 1.3 83.8 - - - +
110Y ALA* 1.3 61.1 + - - +
112Y ASN* 4.0 10.0 - - - +
98Z ASN* 3.5 16.9 - - - +
101Z ASN* 4.2 5.8 + - - +
102Z GLY* 2.9 21.9 - - - -
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Residues in contact with ALA 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Y TYR* 2.8 25.2 + - + +
109Y SER* 1.3 79.7 + - - +
111Y PHE* 1.3 63.2 + - + +
112Y ASN* 3.6 1.9 + - - -
98Z ASN* 3.6 13.0 - - - +
99Z MET* 3.9 34.2 - - - +
102Z GLY* 4.1 4.7 - - - -
69b THR* 2.6 34.5 + - - +
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Residues in contact with PHE 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1917 A 3.8 24.0 - - - -
75Y ILE* 4.8 12.9 - - + +
106Y TYR* 3.7 34.3 - + - -
107Y TYR* 3.1 48.2 + + + +
110Y ALA* 1.3 79.8 - - + +
112Y ASN* 1.3 74.9 + - - +
113Y ALA* 3.2 2.2 + - - +
99Z MET* 3.7 26.9 - - + -
69b THR* 3.4 17.5 - - - +
70b GLY* 3.5 32.1 - - - -
71b PRO* 4.6 3.4 - - + -
72b 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
------------------------------------------------------------
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