Contacts of the strand formed by residues 120 - 126 (chain C) in PDB entry 2E9S
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 ILE 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C THR 3.0 8.8 + - - +
88C VAL* 3.2 14.2 - - + +
89C ALA 2.8 26.2 + - - +
119C VAL* 1.3 79.2 - - - +
121C ILE* 1.3 65.0 + - - +
151C MET* 4.4 16.4 - - + -
170C VAL* 4.0 9.2 - - + +
173C ALA* 3.3 40.2 - - + +
174C LEU* 3.4 39.0 - - + +
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.3 11.7 - - + +
91C VAL* 4.2 18.8 - - + -
108C ILE* 4.5 11.0 - - + -
111C VAL* 3.8 29.8 - - + -
112C ARG* 3.7 36.3 - - - +
119C VAL* 4.0 11.1 + - + +
120C ILE* 1.3 81.4 - - - +
122C MET* 1.3 68.6 + - - +
123C LEU 4.5 0.4 - - - +
150C VAL* 3.6 26.0 - - + +
151C MET* 2.8 32.2 + - - +
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Residues in contact with MET 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA 3.0 9.9 + - - +
90C VAL* 3.4 5.8 - - - -
91C VAL 2.9 25.9 + - - +
120C ILE* 4.2 0.6 + - - +
121C ILE* 1.3 75.2 - - - +
123C LEU* 1.3 59.0 + - - +
124C VAL* 3.7 10.0 + - + +
151C MET* 3.6 25.6 - - + +
152C PHE 3.7 24.5 - - - -
153C ILE* 3.9 6.1 - - + -
166C LEU* 3.3 28.9 - - + +
169C ARG* 3.9 40.8 - - + +
170C VAL* 4.0 26.7 - - + -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 3.4 20.6 - - + +
93C TYR* 3.9 16.4 - - + -
101C PHE* 4.8 3.1 - - + -
104C THR* 3.8 33.0 - - + -
108C ILE* 4.4 8.1 - - + -
121C ILE* 4.0 2.2 - - + +
122C MET* 1.3 72.3 - - - +
124C VAL* 1.3 59.7 + - - +
141C GLY 3.9 11.4 - - - +
144C ARG* 4.3 14.1 - - + -
145C ALA* 4.1 14.8 - - + +
150C VAL* 4.0 11.9 - - + -
151C MET 2.8 15.8 + - - +
152C PHE* 3.3 23.9 - - + -
153C ILE 3.1 24.4 + - - -
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 4.3 5.6 - - + -
90C VAL* 3.6 29.4 - - + -
91C VAL 2.8 11.9 + - - +
92C VAL* 4.1 14.4 - - + -
93C TYR* 2.9 35.5 + - - +
122C MET* 3.7 15.3 - - + -
123C LEU* 1.3 76.9 - - - +
125C GLY* 1.3 63.6 + - - +
126C ASN* 4.0 2.0 - - + +
153C ILE* 3.3 6.7 - - + +
155C THR* 3.3 36.1 - - + +
166C LEU* 3.8 11.0 - - + -
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Residues in contact with GLY 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C TYR* 3.5 32.9 + - - -
95C ILE* 3.7 8.6 - - - +
123C LEU 4.2 0.2 + - - -
124C VAL* 1.3 70.8 - - - +
126C ASN* 1.3 62.0 + - - -
128C THR* 4.0 0.9 - - - +
152C PHE* 4.4 0.6 - - - -
153C ILE 2.9 13.1 + - - -
154C GLU* 3.1 13.3 - - - +
155C THR 2.9 23.3 + - - +
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Residues in contact with ASN 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL 3.0 20.4 + - - +
25C GLY* 3.7 8.5 + - - -
29C LEU* 3.5 10.3 - - - +
92C VAL* 3.7 15.3 - - + -
93C TYR 2.9 16.5 + - - +
94C ASP* 3.7 0.9 - - - -
95C ILE* 3.0 23.1 + - - +
124C VAL* 3.4 1.0 + - + -
125C GLY* 1.3 72.9 - - - +
127C LYS* 1.3 83.1 + - - +
155C THR* 2.9 31.7 + - - +
157C ALA 3.5 12.6 + - - -
802C GDP 3.1 26.2 + - - -
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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