Contacts of the strand formed by residues 112 - 122 (chain U) in PDB entry 4N3E
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 112 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U GLU* 3.8 3.5 - - - +
12U SER* 3.1 31.6 + - - +
14U ILE 2.2 28.8 + - - -
15U ALA 3.9 2.6 + - - -
16U PRO* 3.9 18.4 - - - +
19U LEU* 4.1 17.1 - - - +
105U LEU* 5.1 2.9 - - - -
106U GLU 3.5 12.8 - - - -
108U VAL* 4.0 8.9 + - - +
111U GLY* 1.3 74.2 - - - -
113U LYS* 1.3 67.8 + - - +
201U 2AN 5.3 1.1 - - - -
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Residues in contact with LYS 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U GLU* 4.1 21.5 + - + +
10U GLU 3.5 13.2 - - - +
11U GLU* 4.3 18.8 - - + +
105U LEU* 3.5 8.3 - - - +
106U GLU* 2.7 62.9 + - + +
108U VAL* 4.0 16.8 - - + -
112U SER* 1.3 75.8 - - - +
114U GLY* 1.3 61.5 + - - +
201U 2AN 4.3 4.9 - - - -
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Residues in contact with GLY 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U GLU* 3.0 8.4 - - - +
10U GLU 2.9 33.6 + - - -
104U LYS 3.3 10.3 - - - -
105U LEU* 3.7 11.2 - - - -
106U GLU* 6.0 0.2 - - - -
113U LYS* 1.3 81.0 - - - +
115U LYS* 1.3 60.5 + - - -
116U ILE* 3.7 7.5 - - - +
201U 2AN 3.9 4.7 - - - -
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Residues in contact with LYS 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U VAL* 4.5 15.9 - - + -
8U LYS 3.5 12.8 - - - +
9U GLU* 4.4 12.8 - - + +
102U GLU 3.4 6.1 - - - +
103U VAL* 3.7 0.5 - - - -
104U LYS* 3.0 39.7 + - + +
114U GLY* 1.3 73.4 - - - -
116U ILE* 1.3 59.7 + - - +
117U THR* 3.5 21.5 - - - +
83V LYS* 4.4 22.0 - - - +
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Residues in contact with ILE 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6U ILE 3.7 1.9 - - - +
8U LYS* 3.1 44.3 + - + +
10U GLU* 4.5 4.9 - - + +
101U TYR* 5.7 1.1 - - + -
102U GLU 3.4 6.5 - - - +
103U VAL* 4.4 9.6 - - + -
104U LYS 5.5 0.2 - - - +
105U LEU* 5.4 0.9 - - + -
114U GLY 3.7 15.0 - - - +
115U LYS* 1.3 74.1 - - - +
117U THR* 1.3 67.0 + - - +
118U VAL* 4.1 15.0 - - + +
201U 2AN 3.2 93.1 - - + +
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Residues in contact with THR 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U THR* 3.6 27.1 - - + -
6U ILE 3.3 3.4 - - - -
7U VAL* 3.7 13.1 - - + +
100U VAL 3.8 1.6 - - - +
101U TYR* 3.6 1.9 - - - -
102U GLU* 2.9 50.5 + - + +
115U LYS* 3.5 25.5 - - - +
116U ILE* 1.3 74.7 + - - +
118U VAL* 1.3 66.8 + - - +
119U THR* 4.4 4.7 - - - +
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Residues in contact with VAL 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U TYR 3.8 1.2 - - - +
5U THR* 3.2 4.3 - - - +
6U ILE* 2.8 53.3 + - + +
8U LYS* 6.1 1.8 - - - -
99U VAL* 3.6 29.6 - - + -
100U VAL 3.5 2.7 - - - +
101U TYR* 3.8 26.7 - - + -
116U ILE* 4.1 17.3 - - + -
117U THR* 1.3 77.5 - - - +
119U THR* 1.3 60.4 + - - +
120U TYR* 3.7 18.0 - - + +
137U GLU* 6.3 3.6 - - + -
201U 2AN 4.9 5.2 - - + -
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Residues in contact with THR 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U ALA* 3.5 24.2 - - + -
4U TYR 3.7 2.7 - - - -
5U THR* 3.4 23.7 + - - +
98U LYS 3.9 0.3 - - - +
99U VAL* 3.3 4.4 - - - +
100U VAL* 2.8 47.0 + - - +
117U THR* 4.1 4.7 - - - +
118U VAL* 1.3 71.7 - - - +
120U TYR* 1.3 63.8 + - - +
121U HIS* 3.4 29.7 + - + +
5V THR* 5.6 3.8 - - + +
7V VAL* 5.8 2.5 - - + -
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Residues in contact with TYR 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U ALA* 3.4 6.3 - - - +
4U TYR 2.8 40.5 + - - +
6U ILE* 4.4 11.7 - - + -
96U ILE* 4.6 8.5 - - + -
98U LYS 3.9 3.1 - - - -
99U VAL* 3.6 23.2 - - + +
101U TYR* 5.1 1.4 + - - -
118U VAL* 3.7 24.9 - - + +
119U THR* 1.3 73.8 - - - +
121U HIS* 1.3 62.2 + - - +
128U VAL* 3.8 19.7 - - + +
132U GLU* 3.4 51.6 + - + -
133U VAL* 3.8 21.6 - - + -
136U GLY* 3.7 20.4 - - - -
137U GLU 4.3 0.7 + - - -
202U 2AN 3.9 8.0 - + - -
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Residues in contact with HIS 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U ALA* 4.1 10.8 - - + +
96U ILE* 3.4 6.9 - - - +
97U GLU* 2.7 37.3 + - + +
98U LYS* 2.8 48.5 + - + +
100U VAL* 3.8 27.3 - - + +
119U THR* 3.4 28.3 - - + +
120U TYR* 1.3 72.1 - - - +
122U PRO* 1.3 63.4 - - + +
7V VAL* 5.2 13.2 - - + -
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Residues in contact with PRO 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1U MET* 5.7 4.9 - - - +
2U ALA 3.9 27.8 - - - +
3U ALA* 4.5 3.1 - - - -
95U ASN 3.3 11.9 - - - +
96U ILE* 4.2 2.2 - - + -
97U GLU* 3.6 12.4 - - - +
120U TYR 4.1 3.8 - - - +
121U HIS* 1.3 89.5 - - + +
123U LYS* 1.3 62.6 + - - +
124U PRO* 3.7 3.3 - - + +
126U CYS 3.4 25.8 - - - +
127U THR* 4.2 1.6 - - - +
128U VAL* 4.1 13.2 - - + -
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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