Contacts of the strand formed by residues 111 - 115 (chain A) in PDB entry 2JRI
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.9 14.2 + - - -
24A GLN* 5.5 1.6 + - - +
110A ARG* 1.3 89.6 + - - +
112A PHE* 1.3 63.1 + - - +
113A ILE* 5.8 1.6 - - - -
123A VAL 3.6 14.1 - - - -
124A ARG* 3.2 17.5 - - - +
125A LYS 4.1 0.3 + - - -
130A TRP* 3.9 4.4 - - - -
164A VAL* 3.9 2.4 - - - +
165A VAL* 2.9 35.2 + - - +
169A LEU* 3.6 21.6 - - - +
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Residues in contact with PHE 112 (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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106A PRO* 5.1 5.2 - - + -
109A GLU* 5.6 3.4 - - + -
111A SER* 1.3 74.6 - - - +
113A ILE* 1.3 63.9 + - - +
114A CYS* 3.6 23.8 - - - -
121A PHE 3.9 0.2 - - - +
123A VAL* 2.9 48.9 + - + +
130A TRP* 3.5 35.0 - + - -
148A LEU* 3.8 13.9 - - + -
151A PHE* 4.5 2.7 - + - -
152A LEU* 3.5 31.4 - - + -
155A LEU* 4.2 7.0 - - + -
162A ILE* 3.7 17.9 - - + -
163A PHE 3.1 13.7 - - - +
164A VAL* 3.7 20.9 - - + -
165A VAL* 4.9 0.4 - - - -
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Residues in contact with ILE 113 (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 CYS* 4.3 4.9 - - - -
22A LEU* 3.7 28.7 - - + -
80A ILE* 4.9 11.9 - - + -
111A SER* 5.8 1.1 - - - -
112A PHE* 1.3 82.5 - - - +
114A CYS* 1.3 65.0 + - - +
120A TRP* 3.7 29.4 - - + -
121A PHE 3.4 8.3 - - - +
122A THR* 3.7 30.5 - - + -
123A VAL 4.3 2.7 - - - +
161A SER 3.2 3.3 - - - +
162A ILE* 3.5 1.0 - - - -
163A PHE* 2.8 50.1 + - + +
165A VAL* 5.6 4.0 - - + -
256B ARG* 4.2 11.2 - - - +
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Residues in contact with CYS 114 (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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112A PHE* 3.6 22.9 - - - -
113A ILE* 1.3 75.8 - - - +
115A ASN* 1.3 60.3 + - - +
120A TRP* 2.9 9.2 - - - +
121A PHE* 2.7 54.6 + - + -
123A VAL* 3.9 4.7 - - - -
151A PHE* 4.6 0.2 - - - -
155A LEU* 3.5 29.6 - - + -
160A TYR* 3.4 23.2 - - + -
161A SER 3.3 4.9 - - - -
162A ILE* 4.5 2.5 - - + +
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Residues in contact with ASN 115 (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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114A CYS* 1.3 75.1 - - - +
116A TYR* 1.3 59.4 + - - +
117A LYS* 3.1 20.0 + - - +
119A HIS 3.8 2.5 - - - -
120A TRP* 3.2 33.5 - - + +
159A GLY 3.7 1.2 - - - +
160A TYR* 3.2 6.8 - - - -
161A SER* 2.7 59.2 + - - +
163A PHE* 3.5 24.4 - - + -
191B THR* 2.8 33.6 + - - +
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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