Contacts of the strand formed by residues 105 - 112 (chain B) in PDB entry 1ESG
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 LEU 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B GLU* 3.7 28.5 - - + +
99B PHE 3.7 3.8 - - - +
100B ILE* 3.8 25.8 - - + -
104B GLU* 1.3 81.4 - - - +
106B LYS* 1.3 74.5 + - - +
107B ARG* 3.6 35.7 - - - +
137B ASP* 4.2 4.2 - - - +
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.8 8.9 - - + +
19B ASP* 2.6 24.8 + - - +
22B ILE* 4.3 10.8 - - + -
97B LYS 4.0 0.2 - - - +
98B GLU* 3.4 3.1 - - - -
99B PHE* 2.9 51.0 + - + +
101B GLU* 3.6 30.3 - - + +
104B GLU* 3.7 32.5 + - + +
105B LEU* 1.3 81.7 - - - +
107B ARG* 1.3 63.4 + - - +
137B ASP* 3.2 20.4 - - + +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 5.1 0.2 - - - -
96B TYR* 3.6 31.0 - - + -
97B LYS 3.1 16.6 - - - +
98B GLU* 3.0 31.3 + - + -
99B PHE* 5.2 0.4 - - - -
105B LEU* 3.6 27.1 - - + +
106B LYS* 1.3 74.4 - - - +
108B VAL* 1.3 64.0 + - - +
109B GLY 4.2 0.2 - - - -
134B GLY 5.1 1.0 + - - -
135B GLU* 2.8 52.6 + - - +
136B ILE* 3.5 7.6 - - + -
137B ASP* 2.7 39.2 + - - +
138B LEU 3.6 1.2 + - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 3.7 28.7 - - + -
25B ALA* 3.8 25.6 - - + -
74B TRP* 3.6 15.6 - - + -
96B TYR* 3.1 7.3 - - - -
97B LYS 2.9 30.1 + - - +
99B PHE* 4.3 4.9 - - + -
107B ARG* 1.3 76.4 - - - +
109B GLY* 1.3 63.0 + - - +
136B ILE* 4.5 0.7 - - - -
138B LEU* 3.4 24.5 - - + +
140B ILE* 3.8 29.2 - - + -
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Residues in contact with GLY 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.0 13.0 - - - -
95B VAL 3.6 7.2 - - - -
96B TYR* 4.1 3.6 - - - -
108B VAL* 1.3 74.7 - - - +
110B MET* 1.3 62.2 + - - +
127B LEU* 4.3 4.6 - - - +
136B ILE* 4.0 16.5 - - - +
138B LEU 3.0 11.1 + - - +
139B ALA* 3.5 4.0 - - - -
140B ILE* 2.9 24.6 + - - +
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Residues in contact with MET 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 4.5 9.0 - - + -
64B CYS* 4.1 2.9 - - - -
65B TYR* 3.8 18.8 - - + -
68B LEU* 3.2 35.0 - - + -
74B TRP* 4.1 13.0 - - + -
93B ILE* 3.8 2.1 - - - +
94B ASP* 3.9 0.7 - - - +
95B VAL* 2.9 39.1 + - + +
108B VAL 4.2 0.2 + - - -
109B GLY* 1.3 74.6 - - - +
111B GLU* 1.3 99.4 + - - +
112B PHE 3.7 3.6 - - - -
127B LEU* 4.9 1.1 - - - -
140B ILE* 3.2 33.2 - - + +
142B LEU* 3.9 26.5 - - + -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 3.6 6.1 - - - +
93B ILE* 3.4 6.9 - - + -
94B ASP* 2.8 36.5 + - + +
110B MET* 1.3 85.4 - - - +
112B PHE* 1.3 60.5 + - - +
113B GLU* 3.8 5.7 - - - +
123B SER* 2.5 45.0 + - - +
126B LYS* 3.0 30.1 + - - -
127B LEU* 4.1 15.0 - - + -
140B ILE 3.0 6.9 + - - -
141B ILE* 3.3 5.5 - - - -
142B LEU 3.0 23.0 + - - -
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 3.7 21.3 - - + -
57B VAL* 4.0 7.0 - - + -
60B ILE* 4.0 13.2 - - + -
61B LYS* 3.6 48.5 + - + -
64B CYS* 4.1 9.4 - - + -
65B TYR* 2.9 24.7 + - + +
94B ASP* 4.5 2.8 - - - +
110B MET* 3.7 3.1 - - - -
111B GLU* 1.3 71.7 - - - +
113B GLU* 1.3 70.3 + - - +
114B THR* 3.4 26.1 + - + -
142B LEU* 3.6 27.6 - - + -
144B PRO* 5.0 0.2 - - + -
179B PHE* 3.4 33.0 - + - -
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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