Contacts of the helix formed by residues 102 - 118 (chain J) in PDB entry 5AK9
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 ASN 102 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J SER* 5.5 1.6 + - - -
100J LEU 3.3 3.9 + - - +
101J PHE* 1.3 74.1 - - - +
103J MET* 1.3 59.0 + - - +
104J ARG* 3.2 14.5 + - - +
105J GLU* 2.9 48.0 + - - +
106J GLN* 2.8 30.5 + - - +
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Residues in contact with MET 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J ASN* 1.3 76.4 - - - +
104J ARG* 1.3 65.7 + - - +
106J GLN* 2.9 18.9 + - - +
107J ILE* 2.9 51.0 + - + +
145J LEU* 3.5 27.4 - - + -
176J THR* 5.5 3.1 - - + -
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Residues in contact with ARG 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J GLU 3.0 44.3 + - - +
6J ASN* 4.6 8.7 + - - +
8J SER* 4.9 5.2 - - - -
9J GLY* 4.6 12.1 - - - -
102J ASN* 3.2 10.0 + - - +
103J MET* 1.3 77.4 - - - +
105J GLU* 1.3 64.0 + - + +
107J ILE* 3.4 8.2 + - - +
108J ALA* 3.1 22.7 + - + +
181J HIS* 3.8 36.4 + - + +
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Residues in contact with GLU 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J SER* 3.8 39.8 - - - +
9J GLY* 5.2 0.9 - - - +
12J ALA* 3.5 11.7 - - + +
94J MET* 4.7 7.3 - - - +
100J LEU 4.5 1.2 - - - +
101J PHE* 3.4 30.8 - - + -
102J ASN* 2.9 45.4 + - - +
104J ARG* 1.3 79.1 - - + +
106J GLN* 1.3 64.4 + - - +
108J ALA* 3.3 1.0 + - - -
109J PHE* 2.9 26.5 + - - +
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Residues in contact with GLN 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J PHE* 2.7 26.7 + - + +
102J ASN* 2.8 23.7 + - - +
103J MET* 2.9 15.0 + - - +
105J GLU* 1.3 71.1 - - - +
107J ILE* 1.3 66.0 + - + +
109J PHE* 3.5 0.7 + - - +
110J ILE* 3.0 32.1 + - + +
141J TRP* 3.4 64.9 - - + +
144J ASN* 5.7 2.8 - - - +
145J LEU* 4.5 11.2 - - + +
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Residues in contact with ILE 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J MET* 2.9 52.4 + - + +
104J ARG* 3.8 6.5 - - - +
106J GLN* 1.3 76.9 - - - +
108J ALA* 1.3 63.0 + - - +
110J ILE* 3.3 4.4 + - - +
111J LYS* 3.0 33.6 + - - +
145J LEU* 4.5 14.1 - - + -
176J THR* 4.0 28.3 - - + +
177J ILE* 4.1 27.5 - - + +
180J SER* 4.6 6.5 - - - +
181J HIS 5.2 1.8 - - - +
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J GLY* 3.3 32.3 - - - +
12J ALA* 3.9 3.1 - - + -
13J TYR* 3.5 17.9 - - + +
104J ARG 3.1 16.5 + - - +
105J GLU 3.8 3.4 - - - +
106J GLN 3.3 0.2 - - - -
107J ILE* 1.3 77.4 - - - +
109J PHE* 1.3 64.5 + - - +
111J LYS* 3.3 16.3 - - - +
112J GLY 3.0 18.7 + - - -
181J HIS 5.2 2.7 + - - +
182J LEU* 4.7 6.3 - - + -
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Residues in contact with PHE 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J ALA* 3.4 22.1 - - + +
15J LEU* 4.0 20.9 - - + -
16J GLY* 3.8 22.0 - - - -
19J ILE* 4.3 12.8 - - + -
95J LEU* 5.4 0.2 - - + -
98J ILE* 3.8 20.2 - - + -
101J PHE* 4.1 21.5 - + + -
105J GLU 2.9 16.8 + - - +
106J GLN 3.9 3.4 - - - +
108J ALA* 1.3 77.1 - - - +
110J ILE* 1.3 60.3 + - - +
112J GLY* 3.2 1.4 + - - -
113J LEU* 2.8 47.9 + - + +
134J LEU* 3.9 24.5 - - + -
138J VAL* 4.2 8.3 - - + -
141J TRP* 4.1 15.0 - + + -
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Residues in contact with ILE 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106J GLN* 3.0 22.1 + - + +
107J ILE 3.9 2.9 - - - +
109J PHE* 1.3 76.5 - - + +
111J LYS* 1.3 57.1 + - - +
113J LEU* 3.8 6.2 - - - +
114J TYR* 2.8 33.8 + - - +
127J ILE* 4.8 9.6 - - + -
138J VAL* 4.3 20.9 - - + -
141J TRP* 3.9 33.0 - - + -
142J LEU* 4.0 22.2 - - + -
145J LEU* 4.9 2.7 - - + -
173J PHE* 4.5 11.2 - - + -
177J ILE* 3.9 28.3 - - + -
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Residues in contact with LYS 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J TYR* 3.9 7.4 - - + -
107J ILE* 3.0 20.0 + - - +
108J ALA* 3.3 15.8 - - - +
110J ILE* 1.3 76.9 - - - +
112J GLY* 1.3 56.4 + - - +
114J TYR* 3.8 1.2 - - - +
115J VAL* 2.9 34.0 + - - +
177J ILE* 3.0 34.0 - - - +
178J LEU* 3.8 8.4 - - + +
180J SER* 2.6 29.5 + - - +
181J HIS 2.8 26.5 + - - -
182J LEU* 3.2 20.0 - - - +
184J PRO* 3.3 29.8 - - + -
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Residues in contact with GLY 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J TYR* 3.5 35.3 - - - -
16J GLY 3.8 6.5 - - - -
17J LEU* 3.5 14.4 - - - +
108J ALA 3.0 11.3 + - - -
109J PHE 3.6 2.7 - - - -
111J LYS* 1.3 72.6 - - - +
113J LEU* 1.3 64.7 + - - +
115J VAL 3.3 1.4 + - - -
116J ALA* 3.0 19.4 + - - +
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Residues in contact with LEU 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLY* 3.6 19.8 - - - +
19J ILE* 4.3 14.8 - - + -
20J GLY* 4.3 7.2 - - - +
109J PHE* 2.8 31.6 + - + +
110J ILE* 3.8 5.8 - - - +
112J GLY* 1.3 70.6 - - - +
114J TYR* 1.3 52.1 + - - +
116J ALA* 3.1 2.0 + - - -
117J GLU* 2.7 51.8 + - + +
127J ILE* 4.1 26.7 - - + -
129J ASN* 5.1 2.7 - - + +
134J LEU* 4.6 13.7 - - + -
135J LEU* 4.9 5.4 - - + -
138J VAL* 4.0 27.4 - - + -
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Residues in contact with TYR 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ILE 2.8 22.6 + - - +
111J LYS 3.8 2.9 - - - +
113J LEU* 1.3 71.6 - - - +
115J VAL* 1.3 67.2 + - - +
117J GLU 4.9 0.2 - - - -
118J GLY* 2.8 30.4 + - - +
119J ASP 2.8 30.3 + - - -
120J MET* 4.0 12.4 - - - +
122J LEU* 3.6 13.6 - - + +
125J LEU* 3.4 18.0 - - + +
126J ARG 3.4 35.0 + - - -
127J ILE* 3.6 28.2 - - + +
165J ILE* 4.5 4.0 - - + -
173J PHE* 3.8 24.2 - + + -
178J LEU* 4.0 22.2 - - + -
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Residues in contact with VAL 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J TYR* 3.9 9.2 - - - +
17J LEU* 3.8 18.8 - - + -
21J ASP* 4.9 0.5 - - - +
47J LEU* 5.4 12.3 - - + -
51J HIS* 6.0 1.8 - - + +
111J LYS 2.9 22.2 + - - +
112J GLY 3.5 4.7 - - - +
114J TYR* 1.3 75.8 - - - +
116J ALA* 1.3 61.3 + - - +
118J GLY 4.8 1.4 + - - +
120J MET* 4.3 28.4 - - + +
178J LEU* 5.5 2.5 - - + -
184J PRO* 3.5 32.8 - - + -
185J LEU 5.0 4.0 - - - +
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Residues in contact with ALA 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J GLY 4.5 0.4 - - - +
17J LEU* 4.2 13.5 - - + +
20J GLY* 4.1 7.4 - - - -
21J ASP* 3.3 41.1 - - + +
112J GLY 3.0 15.7 + - - +
113J LEU 3.8 2.5 - - - +
114J TYR 3.0 0.2 - - - -
115J VAL* 1.3 79.9 - - - +
117J GLU* 1.3 59.4 + - - +
118J GLY 3.7 0.7 - - - -
1187J MN 2.4 27.9 + - - -
16N C 2.8 8.8 + - - +
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Residues in contact with GLU 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLY* 3.3 20.3 - - - +
21J ASP* 3.9 0.3 - - - +
113J LEU* 2.7 27.0 + - + +
116J ALA* 1.3 78.7 - - - +
118J GLY* 1.3 58.4 + - - +
127J ILE* 4.0 9.4 - - + -
128J TRP* 3.0 49.6 + - - +
129J ASN* 2.7 30.5 + - - -
1188J MN 2.7 27.8 + - - -
15L G 3.1 10.6 - - - -
15N C 3.1 15.8 + - - +
16N C 3.8 10.6 - - - +
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Residues in contact with GLY 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LEU 4.1 0.2 + - - -
114J TYR* 2.8 30.5 + - - +
115J VAL 5.3 0.9 - - - +
116J ALA 3.7 1.2 - - - -
117J GLU* 1.3 80.4 - - - +
119J ASP* 1.3 60.8 + - - -
120J MET* 2.8 16.3 + - - +
126J ARG 2.8 12.6 - - - -
127J ILE* 4.2 1.6 - - - -
128J TRP* 3.9 3.4 - - - -
16N C 3.8 7.6 - - - +
17N C 3.5 5.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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