Contacts of the strand formed by residues 122 - 129 (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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A THR* 2.7 44.5 + - - +
120A GLU 3.5 1.2 - - - -
121A GLU* 1.3 79.4 - - - +
123A ASN* 1.3 66.8 + - - -
321A VAL* 3.4 3.0 - - - +
359A PRO* 4.9 0.4 - - - -
361A ALA* 3.8 4.1 - - - +
12C GLN 3.1 14.6 - - - -
13C GLY* 3.3 13.3 + - - -
14C VAL* 4.0 2.9 - - - -
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Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LYS* 3.8 23.8 - - + +
117A PHE 3.3 7.4 - - - +
118A TYR* 3.6 22.0 - - - -
122A GLY* 1.3 73.3 - - - -
124A TRP* 1.3 60.0 - - - +
125A ASP* 4.7 1.8 - - - +
319A VAL* 3.3 22.2 - - + +
320A LEU 4.2 3.3 - - - +
321A VAL* 3.9 7.3 - - - +
352A GLN* 4.4 0.4 - - - +
357A ASN 3.1 27.3 + - - -
359A PRO* 3.2 28.3 - - - +
360A PHE 4.0 0.5 + - - -
12C GLN* 2.9 34.0 + - - +
14C VAL* 4.6 0.9 - - - +
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Residues in contact with TRP 124 (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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80A PHE* 3.6 34.3 - + + -
81A LEU* 5.6 0.7 - - + -
117A PHE* 2.9 75.2 + + + -
119A THR* 5.2 0.4 - - - +
122A GLY 3.8 1.0 + - - -
123A ASN* 1.3 72.3 - - - +
125A ASP* 1.3 83.6 + - - +
126A PHE* 4.2 15.7 - + + +
201A PHE* 6.1 0.4 - - - -
203A TRP* 5.2 2.7 - + - -
215A LEU* 3.7 33.7 - - + -
217A TRP* 5.9 0.2 - + - -
260A LEU* 4.8 12.6 - - + -
319A VAL 3.3 12.6 - - - -
320A LEU* 3.4 23.3 - - + +
321A VAL* 4.2 18.6 - - + +
324A MET* 3.8 24.3 - - + -
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Residues in contact with ASP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 3.5 3.6 - - - +
116A LYS* 2.7 45.6 + - - +
123A ASN* 4.7 0.5 - - - +
124A TRP* 1.3 88.1 + - - +
126A PHE* 1.3 58.5 + - - +
127A VAL* 3.9 8.5 + - + -
314A GLY 4.0 0.3 - - - +
315A PHE* 3.3 11.4 - - + -
316A ASN 2.9 46.7 + - - +
317A PRO* 3.9 9.2 - - - +
319A VAL* 2.9 24.2 + - - +
12C GLN* 5.4 0.7 + - - -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.2 30.7 - + + -
114A SER* 3.2 3.3 - - - -
115A VAL* 2.7 46.2 + - + +
117A PHE* 4.2 14.6 - - + -
124A TRP* 3.8 14.4 + + + +
125A ASP* 1.3 72.5 - - - +
127A VAL* 1.3 61.6 + - - +
128A GLY* 3.5 9.4 - - - -
196A SER* 3.5 25.4 - - - -
197A SER* 3.7 13.7 - - - -
201A PHE* 6.4 0.9 - + - -
215A LEU* 3.7 41.3 - - + -
217A TRP* 3.3 41.7 - + + +
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Residues in contact with VAL 127 (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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113A PHE 3.9 2.5 - - - -
114A SER* 3.7 14.1 - - - +
125A ASP* 3.9 6.1 + - + -
126A PHE* 1.3 82.3 - - - +
128A GLY* 1.3 57.2 + - - +
197A SER* 4.7 4.0 - - - +
201A PHE* 6.0 0.7 - - - -
315A PHE* 3.3 30.7 - - + -
316A ASN 3.8 11.4 - - - +
317A PRO* 3.9 18.4 - - + +
335A ARG* 2.8 45.5 + - - +
339A TYR* 3.8 14.6 - - + -
501A HEM 3.8 20.0 - - + -
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 2.8 38.9 + - - -
126A PHE* 3.5 8.5 - - - -
127A VAL* 1.3 75.1 - - - +
129A ASN* 1.3 56.7 + - - -
196A SER 3.2 16.8 - - - -
197A SER* 4.7 2.2 - - - -
501A HEM 3.1 22.2 - - - +
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Residues in contact with ASN 129 (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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56A HIS* 3.5 15.1 + - - -
97A VAL* 5.2 0.6 - - - +
110A PRO* 3.8 23.3 - - + +
111A ARG 3.2 5.7 - - - +
112A GLY* 3.3 16.6 + - - -
113A PHE* 4.3 1.8 - - - +
128A GLY* 1.3 78.1 - - - +
130A ASN* 1.3 63.6 + - - +
131A LEU* 3.9 15.5 - - + +
133A VAL 5.8 0.4 - - - +
134A PHE* 3.7 22.0 - - - -
176A MET* 5.2 1.0 - - - +
195A GLY* 4.4 2.7 - - - -
196A SER* 2.8 32.1 + - - -
198A VAL* 4.6 1.5 - - + +
501A HEM 3.5 31.2 - - + +
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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