Contacts of the strand formed by residues 88 - 98 (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 THR 88 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86J GLY 3.6 6.3 + - - -
87J GLU* 1.3 75.1 - - - +
89J ILE* 1.3 66.1 + - - +
113J LYS* 3.5 9.9 - - - +
114J CYS* 3.5 36.2 + - - +
115J SER* 4.6 2.0 - - - -
147J GLU* 4.2 22.0 - - + +
148J HIS 3.3 10.1 - - - +
149J THR* 3.7 16.4 + - - +
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Residues in contact with ILE 89 (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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80J ILE* 3.6 42.2 - - + +
82J SER* 3.8 24.2 - - - +
87J GLU* 3.8 12.5 + - + +
88J THR* 1.3 78.8 - - - +
90J SER* 1.3 64.9 + - - +
112J GLY 3.6 3.4 - - - -
113J LYS* 4.5 2.5 - - + -
147J GLU* 3.3 0.5 - - - +
148J HIS* 2.7 50.9 + - + +
150J VAL* 4.0 12.6 - - + -
154J GLY 3.6 31.2 - - - +
155J CYS 4.1 0.2 - - - +
156J ALA* 3.8 12.9 - - + +
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Residues in contact with SER 90 (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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80J ILE* 3.4 5.4 - - - +
89J ILE* 1.3 71.7 + - - +
91J ALA* 1.3 61.5 + - - +
111J GLU* 3.2 3.0 - - - -
112J GLY 2.9 34.5 + - - -
114J CYS* 2.8 24.2 + - - -
115J SER 3.2 22.3 - - - -
116J LYS* 4.2 1.1 - - - -
119J ALA* 3.8 14.1 - - - -
146J VAL 3.2 10.5 - - - -
147J GLU* 3.2 16.8 - - - +
156J ALA* 3.9 4.7 - - - -
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Residues in contact with ALA 91 (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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78J GLY 3.7 20.0 - - - +
79J TYR* 4.4 2.0 - - - -
90J SER* 1.3 75.1 - - - +
92J ALA* 1.3 60.6 + - - +
110J TYR 3.3 9.9 - - - +
111J GLU* 4.5 0.4 - - + -
119J ALA* 4.6 1.8 - - - -
145J ALA* 3.3 3.3 - - - +
146J VAL* 3.0 30.6 + - + +
156J ALA* 3.7 27.3 - - + +
157J PHE 3.8 1.3 - - - +
158J ALA* 3.7 14.4 - - - +
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Residues in contact with ALA 92 (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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78J GLY* 5.2 0.7 - - - -
91J ALA* 1.3 76.5 - - - +
93J ILE* 1.3 66.8 + - - +
109J GLU* 3.4 4.5 - - - +
110J TYR* 2.8 32.2 + - + +
119J ALA* 3.6 34.5 - - + +
120J GLU* 4.0 0.4 - - - -
123J VAL* 3.6 13.9 - - + -
144J ILE 3.4 11.7 - - - +
145J ALA* 3.7 7.0 - - + -
158J ALA* 3.7 2.7 - - - +
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Residues in contact with ILE 93 (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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20I LEU* 3.6 27.6 - - + -
76J ALA 3.7 22.0 - - - +
77J TYR* 4.1 0.4 - - - -
92J ALA* 1.3 73.1 - - - +
94J SER* 1.3 68.6 + - - +
107J ILE* 4.2 4.7 - - + -
108J MET 3.4 7.0 - - - +
109J GLU* 3.5 29.4 - - + -
123J VAL* 3.9 3.0 - - - +
143J SER* 3.1 5.7 - - - -
144J ILE* 2.9 42.8 + - + +
158J ALA* 3.3 33.0 - - - +
159J ALA* 3.4 3.1 - - - +
160J ALA* 3.8 11.2 - - + +
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Residues in contact with SER 94 (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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93J ILE* 1.3 75.6 - - - +
95J VAL* 1.3 66.1 + - - +
106J LEU 4.3 0.4 - - - -
107J ILE* 3.2 5.9 - - - +
108J MET* 2.9 37.1 + - - +
123J VAL* 2.8 38.2 + - - +
124J ARG* 4.1 1.1 - - - -
127J ALA* 3.4 9.9 - - - +
141J ILE* 3.8 19.7 - - - -
142J GLU 3.2 5.6 - - - -
143J SER* 4.1 2.2 - - - -
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Residues in contact with VAL 95 (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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18I VAL* 4.6 8.7 - - + -
20I LEU* 3.6 30.3 - - + -
55J MET* 3.9 30.7 - - + -
61J ILE* 4.4 16.2 - - + -
94J SER* 1.3 79.6 - - - +
96J ALA* 1.3 68.2 + - - +
97J ILE* 3.6 5.5 + - + +
106J LEU 3.3 6.5 - - - +
107J ILE* 4.1 21.8 - - + -
140J ARG 3.9 0.2 - - - +
141J ILE* 3.3 4.3 - - - -
142J GLU* 2.7 35.7 + - + +
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Residues in contact with ALA 96 (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 0.4 - - - -
95J VAL* 1.3 71.6 - - - +
97J ILE* 1.3 60.1 + - - +
105J GLY* 3.0 9.0 - - - -
106J LEU* 2.8 37.0 + - + +
127J ALA* 3.9 22.7 - - + +
131J PHE* 3.6 27.1 - - + -
138J LEU* 3.6 14.8 - - + -
140J ARG 3.7 4.7 - - - -
141J ILE* 4.1 4.3 - - + -
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Residues in contact with ILE 97 (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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55J MET* 4.2 18.2 - - + -
61J ILE* 3.6 26.2 - - + -
95J VAL* 4.1 8.1 - - + +
96J ALA* 1.3 75.6 - - - +
98J PRO* 1.3 68.6 - - + +
101J LYS* 3.5 17.9 - - - +
105J GLY* 4.7 0.4 - - - -
131J PHE* 4.0 1.8 - - - -
138J LEU* 3.6 4.2 - - - +
139J ASP* 2.8 44.3 + - - +
140J ARG* 2.9 51.2 + - + +
142J GLU* 3.9 6.3 - - + -
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Residues in contact with PRO 98 (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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55J MET* 4.7 4.5 - - + -
97J ILE* 1.3 91.2 - - + +
99J LYS* 1.3 61.1 + - - +
100J ASP 3.5 22.2 - - - +
101J LYS* 2.9 30.5 + - + -
103J LEU* 3.6 22.2 - - + +
104J CYS 3.5 22.7 - - - +
105J GLY* 4.0 7.9 - - - +
131J PHE* 3.6 23.1 - - + -
137J GLU 3.7 2.0 - - - +
139J ASP* 3.5 3.4 - - - +
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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