Contacts of the strand formed by residues 119 - 126 (chain A) in PDB entry 4ES7
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 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A THR* 3.5 14.1 - - - +
27A CYS* 3.9 34.1 - - + +
28A PRO* 4.5 3.8 - - + -
110A LYS* 3.2 9.0 - - - +
111A LYS* 2.9 51.3 + - - +
116A HIS* 3.9 18.4 - - + +
117A GLY 3.7 10.1 - - - +
118A PRO* 1.3 79.7 - - - +
120A ILE* 1.3 62.0 + - - +
121A THR* 5.0 2.3 + - - -
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Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.7 30.3 - - + -
25A SER* 3.3 2.9 + - - -
26A THR* 2.9 53.0 + - + +
108A LEU* 4.2 15.5 - - + -
109A THR 3.3 8.3 - - - +
110A LYS* 4.1 15.7 - - + -
119A THR* 1.3 76.2 - - - +
121A THR* 1.3 72.4 + - - +
146A VAL* 3.7 35.9 - - + +
147A GLY 5.3 0.2 - - - -
148A ILE* 4.1 11.1 - - + +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.1 15.5 - - + -
24A GLY 3.3 12.1 - - - +
25A SER* 2.7 17.4 + - - -
27A CYS* 4.6 3.6 - - - +
30A LEU* 3.6 24.7 - - + +
107A PHE 3.9 0.5 - - - +
108A LEU* 3.4 3.3 - - - -
109A THR* 2.8 44.1 + - - -
119A THR* 5.0 2.1 + - - -
120A ILE* 1.3 77.3 + - - +
122A ALA* 1.3 63.8 + - - +
123A LYS* 4.3 11.7 - - + -
148A ILE* 4.4 0.2 - - - -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.2 7.3 - - - +
24A GLY 2.8 34.7 + - - +
107A PHE 3.4 4.0 - - - -
108A LEU* 3.5 22.2 - - + -
121A THR* 1.3 73.9 - - - +
123A LYS* 1.3 62.3 + - - +
139A PHE* 3.2 20.5 - - + -
143A ALA* 4.1 7.6 - - + -
148A ILE* 3.8 19.4 - - + +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 3.8 18.4 + - - +
22A ALA 3.5 2.2 - - - -
23A ILE* 3.7 30.7 - - + -
30A LEU* 5.9 1.1 - - - -
37A MET* 5.0 7.5 - - - +
105A ALA 3.8 0.9 - - - +
106A ILE* 3.4 5.2 - - - +
107A PHE* 2.9 36.3 + - + +
109A THR* 6.1 0.4 - - - +
121A THR* 4.5 10.8 - - + -
122A ALA* 1.3 78.8 - - - +
124A LEU* 1.3 60.4 + - - +
125A TYR* 3.3 38.5 + - + +
139A PHE* 3.6 4.9 - - - -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 2.9 20.4 + - - -
21A LEU* 2.9 18.8 + - + -
22A ALA* 2.9 23.4 + - + -
104A TYR* 4.3 8.7 - - + -
105A ALA 3.6 10.1 - - - +
106A ILE* 3.7 17.7 - - + -
123A LYS* 1.3 72.5 - - - +
125A TYR* 1.3 72.1 + - - +
131A LEU* 4.0 20.4 - - + -
135A LEU* 4.2 7.6 - - + +
136A LEU* 3.8 30.1 - - + -
139A PHE* 3.6 32.4 - - + -
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.7 31.6 - + + -
19A TYR 3.1 7.4 - - - -
20A ASN* 3.5 32.2 - - + +
21A LEU* 4.5 0.9 - - - +
40A SER* 5.6 0.2 - - - -
42A LEU* 3.6 34.2 - - + +
104A TYR* 3.2 7.4 - - - +
105A ALA* 2.9 33.3 + - + +
107A PHE* 3.4 37.9 - + + -
123A LYS* 3.3 47.3 + - + +
124A LEU* 1.3 76.1 - - - +
126A GLY* 1.3 58.5 + - - +
131A LEU* 3.9 6.7 - - - +
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 3.4 8.4 - - - -
19A TYR 2.8 33.0 + - - -
21A LEU* 3.9 5.2 - - - +
103A GLU 3.2 9.9 - - - -
125A TYR* 1.3 74.8 - - - +
127A ARG* 1.3 61.2 + - - -
128A ALA 3.1 17.6 - - - +
131A LEU* 3.9 11.0 - - - -
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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