Contacts of the helix formed by residues 115 - 135 (chain J) in PDB entry 1N13
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 SER 115 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J THR* 4.6 4.5 - - - -
90J SER* 3.2 5.8 + - - -
114J CYS* 1.3 80.1 - - - +
116J LYS* 1.3 64.3 - - - +
117J LYS* 3.6 22.4 + - - +
118J GLU* 3.2 21.6 + - - +
119J ALA* 3.0 19.6 + - - +
147J GLU* 3.7 11.0 - - - -
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Residues in contact with LYS 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J SER* 3.3 12.1 + - - -
115J SER* 1.3 72.5 - - - +
117J LYS* 1.3 66.0 + - + +
119J ALA* 3.5 0.8 + - - +
120J GLU* 3.1 31.2 + - - +
145J ALA* 3.2 44.7 + - + +
146J VAL* 4.0 6.1 - - - +
147J GLU* 3.0 35.4 + - + +
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Residues in contact with LYS 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J SER* 3.2 19.0 - - - +
116J LYS* 1.3 79.8 - - + +
118J GLU* 1.3 64.4 + - - +
120J GLU* 3.5 4.6 + - - +
121J LYS* 3.0 25.3 + - - +
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Residues in contact with GLU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J TYR* 4.7 7.0 + - + -
114J CYS* 3.6 27.2 - - + +
115J SER* 3.2 18.7 + - - +
117J LYS* 1.3 75.7 - - - +
119J ALA* 1.3 61.8 + - - +
121J LYS* 3.3 8.6 + - + +
122J THR* 2.9 43.5 + - - +
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Residues in contact with ALA 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J SER* 3.8 20.2 - - - -
91J ALA 4.6 4.7 - - - +
92J ALA* 3.6 16.4 - - + +
110J TYR* 3.8 21.2 - - + -
114J CYS* 3.9 6.7 - - - -
115J SER 3.0 17.7 + - - +
116J LYS* 3.8 4.3 - - - +
118J GLU* 1.3 77.4 - - - +
120J GLU* 1.3 57.4 + - - +
122J THR* 3.3 2.1 + - - -
123J VAL* 2.9 30.8 + - - +
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Residues in contact with GLU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J ALA* 3.9 3.3 - - - +
116J LYS* 3.1 24.8 + - - +
117J LYS* 4.0 5.0 - - - +
119J ALA* 1.3 72.8 - - - +
121J LYS* 1.3 66.1 + - - +
123J VAL* 3.3 7.6 - - + +
124J ARG* 3.0 36.5 + - - +
143J SER* 2.7 45.8 + - - +
144J ILE* 4.1 4.1 - - - +
145J ALA* 3.8 19.8 + - + +
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Residues in contact with LYS 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J LYS 3.0 18.5 + - - +
118J GLU* 3.6 8.5 - - + +
120J GLU* 1.3 76.9 - - - +
122J THR* 1.3 63.4 + - - +
124J ARG* 3.5 7.6 + - - +
125J GLU* 2.8 61.8 + - + +
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Residues in contact with THR 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G THR* 5.7 4.5 - - + -
110J TYR* 3.9 37.8 + - + +
118J GLU* 2.9 29.2 + - - +
119J ALA 3.7 3.6 - - - -
121J LYS* 1.3 77.0 - - - +
123J VAL* 1.3 58.6 + - - +
125J GLU* 3.2 15.5 + - - +
126J MET* 3.0 39.4 + - + +
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Residues in contact with VAL 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J ALA* 3.6 32.5 - - + +
93J ILE 3.9 6.7 - - - +
94J SER* 2.8 30.7 + - - +
108J MET* 3.3 35.2 - - + +
109J GLU 3.7 10.3 - - - -
110J TYR* 3.9 6.5 - - + +
119J ALA 2.9 11.3 + - - +
120J GLU* 3.3 12.6 - - - +
122J THR* 1.3 76.4 - - - +
124J ARG* 1.3 67.0 + - + +
126J MET* 3.3 9.3 + - - +
127J ALA 3.2 12.6 + - - -
143J SER* 4.7 1.6 - - - -
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Residues in contact with ARG 124 (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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94J SER* 4.1 5.6 - - - -
120J GLU* 3.0 30.2 + - - +
121J LYS* 3.8 6.7 - - - +
123J VAL* 1.3 76.1 - - - +
125J GLU* 1.3 64.4 + - + +
127J ALA* 3.2 2.1 + - - +
128J LYS* 3.0 18.5 + - - +
141J ILE* 2.9 66.9 + - + +
143J SER* 2.9 39.5 + - - +
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Residues in contact with GLU 125 (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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121J LYS* 2.8 49.8 + - + +
122J THR* 3.2 15.5 + - - +
124J ARG* 1.3 79.4 - - + +
126J MET* 1.3 56.1 + - - +
128J LYS* 3.2 12.4 + - + +
129J ILE* 2.9 39.6 + - + +
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Residues in contact with MET 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G THR* 3.8 22.0 - - + +
31G LEU* 3.6 31.6 - - + +
32G ASN* 3.0 38.1 - - - +
108J MET* 3.8 15.5 - - + +
109J GLU 3.6 20.4 - - - +
110J TYR* 4.1 16.6 - - + -
122J THR* 3.0 33.4 + - + +
123J VAL* 3.5 17.0 - - - +
124J ARG 3.2 0.2 - - - -
125J GLU* 1.3 77.9 - - + +
127J ALA* 1.3 56.6 + - - +
129J ILE* 3.4 2.3 + - + -
130J GLY* 3.1 14.9 + - - -
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Residues in contact with ALA 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J SER* 3.4 27.4 - - - +
96J ALA* 3.9 27.9 - - + +
106J LEU* 3.9 9.4 - - - +
108J MET* 3.7 12.7 - - + +
123J VAL 3.2 4.8 + - - -
124J ARG 3.2 7.8 + - - +
126J MET* 1.3 74.4 - - - +
128J LYS* 1.3 65.7 + - - +
130J GLY* 3.2 2.6 + - - -
131J PHE* 3.2 21.0 + - - +
141J ILE* 4.3 4.9 - - + -
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Residues in contact with LYS 128 (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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124J ARG 3.0 11.9 + - - +
125J GLU* 3.2 15.0 + - + +
127J ALA* 1.3 76.3 - - - +
129J ILE* 1.3 60.9 - - + +
131J PHE* 3.2 5.6 + - - +
132J GLU* 3.0 43.9 + - + +
138J LEU* 4.0 27.8 - - + -
141J ILE* 4.1 14.8 - - + +
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Residues in contact with ILE 129 (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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28G GLU* 3.5 51.4 - - + +
29G THR* 5.2 3.1 - - + -
32G ASN* 3.6 28.0 - - + +
125J GLU* 2.9 27.5 + - + +
126J MET* 3.6 5.8 - - + +
127J ALA 3.3 0.2 - - - -
128J LYS* 1.3 76.7 - - + +
130J GLY* 1.3 56.4 + - - +
132J GLU* 3.1 17.6 + - + +
133J MET* 2.9 44.5 + - + +
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Residues in contact with GLY 130 (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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32G ASN* 4.3 4.3 - - - -
35G ASP* 4.0 6.1 - - - -
106J LEU* 3.4 23.1 - - - -
126J MET 3.1 12.2 + - - -
127J ALA 3.2 0.8 + - - -
129J ILE* 1.3 77.9 - - - +
131J PHE* 1.3 58.8 + - - +
133J MET* 3.5 7.1 + - - +
134J ARG* 3.1 38.8 + - - +
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Residues in contact with PHE 131 (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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96J ALA* 3.6 38.8 - - + -
97J ILE 4.0 3.6 - - - -
98J PRO* 3.6 32.1 - - + -
104J CYS 3.6 20.4 - - - -
106J LEU* 3.8 19.7 - - + -
127J ALA 3.2 8.0 + - - +
128J LYS* 3.2 9.0 + - - +
130J GLY* 1.3 75.0 - - - +
132J GLU* 1.3 60.4 + - - +
134J ARG* 3.2 4.9 + - - -
135J GLY 2.8 23.2 + - - -
136J TRP* 3.0 54.5 + + + +
137J GLU 3.8 3.8 - - - -
138J LEU* 3.9 24.7 - - + -
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Residues in contact with GLU 132 (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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63B PRO* 4.8 4.3 - - - +
28G GLU* 4.9 4.0 - - - +
128J LYS* 3.0 36.8 + - + +
129J ILE* 3.1 24.1 + - + +
131J PHE* 1.3 76.2 - - + +
133J MET* 1.3 64.2 + - + +
135J GLY* 3.1 14.0 + - - +
136J TRP 5.4 0.4 - - - -
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Residues in contact with MET 133 (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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63B PRO* 4.1 14.7 - - - +
25G SER* 3.8 4.5 - - - +
26G GLU 3.8 17.5 - - - +
27G GLY* 5.0 2.7 - - - -
32G ASN* 3.5 30.5 - - - +
35G ASP* 5.1 2.9 - - - +
36G GLY* 3.7 20.9 - - - -
39G LEU* 4.6 11.8 - - + +
129J ILE* 2.9 38.9 + - + +
130J GLY* 3.7 10.1 - - - +
132J GLU* 1.3 78.0 - - + +
134J ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 134 (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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63B PRO* 4.0 11.7 - - - +
35G ASP* 2.7 42.6 + - - -
39G LEU* 3.7 25.9 - - + +
44G GLY 3.0 24.2 + - - -
45G ASN* 2.8 18.1 + - - -
54J ILE* 4.1 2.8 - - - +
106J LEU* 3.8 20.4 - - - +
130J GLY 3.1 23.1 + - - +
131J PHE* 3.2 13.6 + - - +
132J GLU 3.2 0.2 - - - -
133J MET* 1.3 77.8 - - - +
135J GLY* 1.3 62.8 + - - +
136J TRP* 3.3 53.7 + - + -
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Residues in contact with GLY 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B PRO* 3.8 20.3 - - - +
131J PHE 2.8 6.2 + - - -
132J GLU* 3.1 14.8 + - - -
133J MET 3.3 0.4 + - - -
134J ARG* 1.3 79.8 - - - +
136J TRP* 1.3 64.3 + - - +
137J GLU* 4.2 1.4 + - - +
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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