Contacts of the strand formed by residues 142 - 147 (chain X) in PDB entry 2EXC
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 VAL 142 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93X LYS 3.5 1.2 - - - +
94X LYS* 3.8 1.2 - - - -
95X LEU* 2.8 55.5 + - + +
98X PRO* 4.5 5.1 - - + +
112X LEU* 5.0 4.5 - - + -
129X VAL* 4.1 6.3 - - + -
130X PHE 3.8 3.1 - - - +
139X PHE* 3.5 26.9 - - + -
140X GLN 4.3 0.4 + - - -
141X ASP* 1.3 72.3 - - - +
143X TYR* 1.3 63.7 + - - +
144X LEU* 3.9 26.6 + - + -
394X ILE* 4.2 9.6 - - + -
398X VAL* 3.4 35.2 - - + -
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Residues in contact with TYR 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X THR 3.8 1.6 + - - -
58X PHE* 3.9 19.5 - + - -
59X THR* 3.2 33.6 + - - -
60X VAL* 4.0 12.3 - - + -
92X ILE* 4.3 8.7 - - + -
93X LYS 3.3 4.0 - - - +
94X LYS* 3.6 45.5 - - + -
128X ASN 3.8 0.7 - - - +
129X VAL* 3.3 6.8 - - - +
130X PHE* 2.9 71.2 + + + +
132X PRO* 3.3 26.8 - - + +
141X ASP* 3.9 16.5 + - + -
142X VAL* 1.3 75.0 - - - +
144X LEU* 1.3 62.8 + - - +
145X VAL* 4.8 0.2 - - - -
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Residues in contact with LEU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ILE* 3.4 3.1 - - - +
93X LYS* 2.7 43.7 + - + +
95X LEU* 4.2 26.0 - - + -
111X GLU* 6.1 2.0 - - + -
112X LEU* 3.7 30.7 - - + -
115X MET* 4.2 24.9 - - + -
126X LEU* 3.8 6.1 - - + -
128X ASN 3.7 2.7 - - - -
129X VAL* 4.0 11.2 - - + -
142X VAL* 3.9 20.0 - - + -
143X TYR* 1.3 73.4 - - - +
145X VAL* 1.3 60.8 + - - +
600X JNK 3.3 25.1 - - + -
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Residues in contact with VAL 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64X TYR* 3.9 30.3 - - + +
83X ASP* 5.5 0.4 - - - +
90X VAL* 4.1 18.2 - - + -
91X ALA 3.3 8.5 - - - +
92X ILE* 3.9 16.8 - - + -
126X LEU* 3.7 0.9 - - - +
127X LEU* 2.7 36.7 + - + -
128X ASN* 2.9 25.2 + - + +
130X PHE* 3.9 27.8 - - + -
144X LEU* 1.3 80.0 - - - +
146X MET* 1.3 57.5 + - - +
600X JNK 3.3 7.3 - - - -
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Residues in contact with MET 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X VAL* 3.3 5.7 - - - +
91X ALA* 2.7 39.6 + - + +
124X ILE* 3.8 20.2 - - + -
125X SER 3.7 16.2 - - - +
127X LEU* 3.8 13.7 - - - -
145X VAL* 1.3 74.2 - - - +
147X GLU* 1.3 76.1 + - + +
149X MET* 4.9 1.1 - - + -
196X VAL* 4.7 2.9 - - + -
204X LYS* 4.3 23.6 - - + -
206X LEU* 3.4 33.7 - - + -
600X JNK 3.6 40.2 - - + -
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Residues in contact with GLU 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X ARG* 3.0 46.0 + - - +
89X ASN 3.5 10.9 - - - +
91X ALA 4.1 0.2 - - - -
125X SER* 4.7 4.5 + - - +
127X LEU* 3.5 13.5 - - + +
146X MET* 1.3 100.0 - - + +
148X LEU* 1.3 66.7 - - - +
149X MET* 3.6 22.7 + - - +
198X LYS* 3.9 17.7 + - - +
204X LYS* 3.6 17.4 - - - -
600X JNK 3.7 2.8 - - - -
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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