Contacts of the strand formed by residues 112 - 119 (chain A) in PDB entry 2J2M
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 GLY 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A HIS* 3.6 5.7 - - - -
93A ARG 4.3 0.2 - - - -
94A PHE* 3.2 23.0 - - - -
95A SER* 2.8 26.2 + - - -
111A ARG* 1.3 72.8 - - - +
113A PHE* 1.3 57.1 + - - -
114A SER 4.1 1.3 - - - -
129A ASN* 3.3 15.5 + - - -
193A MET* 3.5 8.1 - - - +
501A HEM 3.4 16.4 - - - -
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Residues in contact with PHE 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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94A PHE* 3.7 27.4 - + - -
111A ARG 4.4 0.9 - - - +
112A GLY* 1.3 72.8 - - - +
114A SER* 1.3 58.5 + - - +
115A VAL* 3.8 16.8 - - + -
126A PHE* 3.2 19.3 - + + -
128A GLY 2.8 38.8 + - - +
129A ASN 4.4 4.7 - - - -
193A MET* 4.1 7.2 - - + -
194A ARG 3.4 18.2 - - - -
195A GLY* 3.4 20.9 - - - -
217A TRP* 3.4 37.9 - + + -
258A TRP* 3.4 32.1 - + - -
297A MET* 3.9 8.3 - - + -
501A HEM 3.7 1.0 - - - +
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Residues in contact with SER 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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92A ALA* 3.1 6.9 - - - +
93A ARG 2.8 42.0 + - - -
94A PHE* 4.6 0.4 - - - -
113A PHE* 1.3 72.4 - - - +
115A VAL* 1.3 64.7 + - - +
126A PHE 3.2 8.1 - - - -
127A VAL* 3.7 5.4 - - - +
315A PHE* 3.7 29.4 - - - -
501A HEM 3.3 39.0 + - - +
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Residues in contact with VAL 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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90A VAL* 3.7 22.9 - - + -
91A PHE 3.6 4.0 - - - +
92A ALA* 4.0 4.7 - - + -
113A PHE* 3.8 16.2 - - + -
114A SER* 1.3 79.3 - - - +
116A LYS* 1.3 60.2 + - - +
117A PHE* 3.2 39.2 - - + -
125A ASP* 3.5 0.2 - - - -
126A PHE* 2.7 45.1 + - + -
217A TRP* 4.3 4.0 - - + -
297A MET* 3.7 33.7 - - + -
315A PHE* 4.0 3.1 - - - -
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Residues in contact with LYS 116 (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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90A VAL* 3.0 8.3 - - - -
91A PHE* 2.9 36.8 + - + +
115A VAL* 1.3 71.5 - - - +
117A PHE* 1.3 62.6 + - - +
118A TYR* 3.4 41.4 - - + +
123A ASN* 3.8 22.2 - - - +
125A ASP* 2.7 40.4 + - - +
313A VAL* 3.5 18.4 - - + -
314A GLY 3.0 27.5 + - - -
315A PHE* 3.5 12.4 - - + -
352A GLN* 4.9 5.5 + - - -
356A ILE 3.7 2.7 - - - +
357A ASN* 3.7 11.0 + - - +
12C GLN* 5.0 3.0 + - - +
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Residues in contact with PHE 117 (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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66A PHE* 3.6 33.4 - + + -
80A PHE* 4.1 12.6 - + - -
88A VAL* 4.0 11.9 - - + -
89A PRO 3.8 4.0 - - - -
90A VAL* 3.7 10.5 - - + -
115A VAL* 3.2 37.2 - - + -
116A LYS* 1.3 71.0 - - - +
118A TYR* 1.3 60.1 + - - +
119A THR* 3.2 14.0 + - - +
123A ASN* 3.3 6.1 - - - +
124A TRP* 2.9 77.6 + + + +
126A PHE* 4.2 7.9 - - + -
217A TRP* 4.0 20.6 - + - -
260A LEU* 5.2 1.1 - - + -
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Residues in contact with TYR 118 (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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63A HIS* 5.4 3.3 - + - -
88A VAL* 3.6 11.6 - - - +
89A PRO* 3.0 45.5 + - + +
90A VAL 4.1 1.6 - - - -
91A PHE* 3.6 36.8 - - + +
116A LYS* 3.4 27.8 - - + +
117A PHE* 1.3 67.2 - - - +
119A THR* 1.3 62.3 + - - +
123A ASN* 3.6 15.9 - - - +
355A PRO 5.0 2.0 - - - -
356A ILE* 2.6 33.3 + - - +
358A CYS 3.4 26.9 - - - -
360A PHE* 3.9 23.8 - - + +
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Residues in contact with THR 119 (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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79A ALA* 5.1 0.9 - - + +
80A PHE* 3.4 45.5 - - + +
88A VAL* 4.3 6.4 - - - +
117A PHE* 3.2 11.9 + - - +
118A TYR* 1.3 74.9 - - - +
120A GLU* 1.3 66.8 + - + +
121A GLU* 3.0 24.5 - - + +
122A GLY* 2.7 33.1 + - - +
124A TRP* 5.2 0.3 - - - +
321A VAL* 4.0 12.5 - - + +
360A PHE* 4.0 3.6 + - - +
361A ALA 4.0 12.8 + - - -
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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