Contacts of the helix formed by residues 93 - 111 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G THR* 4.6 0.7 - - - -
92I SER* 1.3 76.5 + - - +
94I PRO* 1.3 67.8 - - - -
95I ALA 3.3 1.8 - - - -
96I LEU* 2.7 29.5 + - - +
97I VAL* 3.1 16.1 + - - +
133I VAL* 4.3 19.5 - - - +
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Residues in contact with PRO 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G THR* 3.3 17.5 - - + +
65G GLN* 3.4 28.7 - - + +
66G TYR 4.6 0.4 - - - -
67G GLY* 3.8 10.5 - - - +
92I SER 4.6 0.4 - - - +
93I GLY* 1.3 84.0 - - - -
95I ALA* 1.3 63.5 + - - +
97I VAL* 3.0 13.2 + - + +
98I ASN* 2.9 25.3 + - - +
133I VAL* 4.3 9.3 - - + -
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Residues in contact with ALA 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G THR* 3.3 18.8 + - + +
67G GLY* 3.5 15.4 - - - -
68G ILE 3.7 21.1 - - - +
69G THR* 3.4 13.8 - - + +
90I ILE* 3.5 24.4 - - + +
93I GLY 3.1 0.8 + - - -
94I PRO* 1.3 80.2 - - - +
96I LEU* 1.3 62.7 + - - +
98I ASN* 3.3 1.7 + - - +
99I MET* 3.0 19.1 + - - +
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Residues in contact with LEU 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I VAL* 4.3 6.1 - - + +
86I ALA* 3.9 28.9 - - + +
87I LEU* 3.8 37.0 - - + +
90I ILE* 4.2 5.5 - - + +
91I GLY 3.6 11.6 + - - +
92I SER* 3.9 10.8 - - - -
93I GLY 2.7 17.1 + - - +
95I ALA* 1.3 71.8 - - - +
97I VAL* 1.3 61.9 + - + +
99I MET* 3.1 4.8 + - + +
100I ILE* 2.8 52.7 + - + +
126I THR* 4.6 13.5 - - + -
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Residues in contact with VAL 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I GLY 3.1 7.4 + - - +
94I PRO* 3.2 10.1 - - + +
96I LEU* 1.3 78.3 - - + +
98I ASN* 1.3 65.6 + - - +
100I ILE* 3.3 0.6 + - + -
101I ASN* 3.1 33.2 + - - +
130I THR* 3.4 26.1 + - - +
131I GLY* 3.6 28.7 - - - +
132I TYR 4.8 2.7 - - - +
133I VAL* 3.7 30.7 - - + -
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Residues in contact with ASN 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLY* 3.1 35.2 + - - -
69G THR* 4.4 7.6 - - + -
94I PRO* 2.9 13.5 + - - +
95I ALA* 3.5 7.4 - - - +
96I LEU 3.2 0.2 - - - -
97I VAL* 1.3 79.9 - - - +
99I MET* 1.3 63.6 + - - +
101I ASN* 3.5 9.0 + - - +
102I GLY 3.3 15.6 + - - -
109J SER 3.5 22.9 - - - +
110J ALA* 3.7 3.7 - - - +
112J ASN* 5.2 9.1 + - - +
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Residues in contact with MET 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528 T 4.1 11.2 - - - +
69G THR* 4.6 5.8 - - + -
70G GLY 5.3 0.2 - - - +
82I LYS* 4.7 13.0 - - + -
83I VAL* 6.3 0.4 - - - -
86I ALA* 3.8 24.7 - - + -
90I ILE* 3.7 23.8 - - + -
95I ALA 3.0 13.9 + - - +
96I LEU* 3.1 13.4 + - + +
98I ASN* 1.3 76.3 - - - +
100I ILE* 1.3 61.4 + - + +
102I GLY* 3.2 3.6 + - - -
103I LEU* 2.8 31.8 + - + +
106J TYR* 4.7 9.4 - - - -
110J ALA* 4.2 19.8 + - - +
111J PHE* 3.8 28.7 - - + -
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Residues in contact with ILE 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 5.0 3.1 - - + -
83I VAL* 4.3 18.6 - - + -
96I LEU* 2.8 46.4 + - + +
97I VAL* 3.9 3.4 - - + +
99I MET* 1.3 73.6 - - + +
101I ASN* 1.3 58.1 + - - +
103I LEU* 3.5 7.1 - - + +
104I LYS* 2.8 43.9 + - + +
122I VAL* 4.2 15.3 - - + -
126I THR* 4.1 22.9 - - + -
130I THR* 3.5 35.9 - - + +
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Residues in contact with ASN 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I VAL* 3.1 34.6 + - - +
98I ASN* 3.7 9.9 + - - +
99I MET 3.2 0.2 - - - -
100I ILE* 1.3 77.3 - - - +
102I GLY* 1.3 61.0 + - - +
104I LYS* 3.5 8.2 + - - +
105I GLY* 3.2 17.5 + - - -
130I THR* 3.3 21.2 - - - +
131I GLY* 4.3 7.1 + - - -
109J SER* 4.2 8.6 + - - +
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Residues in contact with GLY 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I ASN 3.3 4.6 + - - -
99I MET 3.2 6.3 + - - -
101I ASN* 1.3 76.6 - - - +
103I LEU* 1.3 59.9 + - - +
105I GLY* 3.1 4.1 + - - -
106I TYR 2.9 24.3 + - - -
106J TYR* 3.5 20.1 - - - -
109J SER* 3.0 23.9 + - - -
110J ALA* 4.0 9.6 - - - -
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Residues in contact with LEU 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 3.6 17.3 - - + -
82I LYS* 3.5 48.7 - - + +
83I VAL* 3.6 30.3 - - + +
99I MET* 2.8 23.0 + - + +
100I ILE* 3.5 8.5 - - + +
102I GLY* 1.3 72.6 - - - +
104I LYS* 1.3 64.5 + - - +
106I TYR* 3.1 11.1 + - + +
107I TYR* 3.0 41.0 + - + -
106J TYR* 3.9 10.1 - - + -
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Residues in contact with LYS 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE* 3.8 29.2 - - + -
100I ILE* 2.8 36.4 + - + +
101I ASN* 3.7 7.3 + - - +
103I LEU* 1.3 71.5 - - - +
105I GLY* 1.3 57.5 + - - +
107I TYR* 3.2 1.4 + - - +
108I ILE* 2.8 55.0 + - + +
115I PRO* 5.0 5.5 - - - +
118I LEU* 4.8 5.8 - - + -
119I ASP* 2.7 36.7 + - - +
122I VAL* 5.0 2.0 - - + -
129I PRO* 6.1 0.2 - - - +
130I THR* 4.6 12.4 - - + +
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Residues in contact with GLY 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I ASN 3.2 8.5 + - - -
102I GLY* 3.1 8.1 + - - -
104I LYS* 1.3 78.1 - - - +
106I TYR* 1.3 57.8 + - - +
108I ILE* 4.5 5.8 - - - +
109I SER* 2.6 36.9 + - - -
102J GLY 4.4 3.4 - - - -
105J GLY* 5.9 2.0 - - - -
106J TYR 5.3 2.5 - - - -
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Residues in contact with TYR 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 3.8 5.2 + - - -
2887 T 2.9 18.1 + - - -
82I LYS* 5.6 4.0 - - - -
102I GLY 2.9 12.1 + - - +
103I LEU* 3.2 15.3 - - + +
105I GLY* 1.3 75.6 - - - +
107I TYR* 1.3 86.3 + + - +
110I ALA* 2.8 41.5 + - + +
111I PHE* 3.7 26.3 - + - -
82J LYS* 2.8 40.5 + - - -
99J MET* 4.6 7.4 - - - +
102J GLY 3.7 14.3 + - - -
103J LEU* 4.0 12.3 - - + -
106J TYR* 3.7 30.5 - + + -
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Residues in contact with TYR 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 4.5 5.0 - - + +
2887 T 3.3 34.0 + - - -
75I ILE* 3.5 38.1 - - + -
78I GLY* 3.5 10.0 - - - -
79I PHE* 3.7 30.3 - + + -
82I LYS* 5.2 1.6 - - + -
103I LEU* 3.0 25.0 + - + +
104I LYS 4.0 1.8 - - - +
106I TYR* 1.3 98.2 - + - +
108I ILE* 1.3 66.9 + - - +
111I PHE* 3.1 40.6 + + - +
113I ALA* 3.0 25.6 + - + +
118I LEU* 4.4 8.1 - - + -
71L PRO* 6.5 1.1 - - + -
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Residues in contact with ILE 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I LYS* 2.8 44.3 + - + +
105I GLY* 4.1 5.6 - - - +
107I TYR* 1.3 72.9 - - - +
109I SER* 1.3 62.7 + - - +
112I ASN* 3.1 24.9 - - - +
113I ALA 3.6 16.5 + - - +
115I PRO* 3.9 32.1 - - + -
118I LEU* 3.3 21.3 - - + -
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Residues in contact with SER 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLY* 2.6 21.4 + - - -
108I ILE* 1.3 84.2 - - - +
110I ALA* 1.3 60.9 + - - +
112I ASN* 4.0 10.9 - - - +
98J ASN* 3.5 16.9 - - - +
101J ASN* 4.2 6.1 + - - +
102J GLY* 2.9 22.2 - - - -
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Residues in contact with ALA 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I TYR* 2.8 25.2 + - + +
109I SER* 1.3 79.4 + - - +
111I PHE* 1.3 62.2 + - + +
112I ASN* 3.6 1.9 + - - -
98J ASN* 3.6 12.6 - - - +
99J MET* 3.9 34.8 + - - +
102J GLY* 4.1 5.2 - - - -
69L THR* 2.6 34.1 + - - +
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Residues in contact with PHE 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2877 A 3.8 24.0 - - - -
75I ILE* 4.8 13.7 - - + +
106I TYR* 3.7 33.4 - + - -
107I TYR* 3.1 48.2 + + + +
110I ALA* 1.3 79.6 - - + +
112I ASN* 1.3 74.1 + - - +
113I ALA* 3.3 2.0 + - - +
99J MET* 3.7 28.3 - - + -
69L THR* 3.4 17.3 - - - +
70L GLY* 3.5 31.4 - - - -
71L PRO* 4.6 3.4 - - + -
72L ASN* 3.3 19.3 + - - +
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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