Contacts of the strand formed by residues 292 - 302 (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 GLN 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A MET* 5.3 5.3 - - + +
74A LYS* 5.1 3.1 + - - -
75A TYR* 3.1 39.0 + - - -
261A PHE* 3.2 3.2 - - - -
262A VAL* 2.9 47.0 + - + +
264A VAL* 3.9 18.2 - - - +
290A PRO* 4.3 12.6 + - + +
291A PHE* 1.3 79.0 - - - +
293A HIS* 1.3 66.0 + - - +
294A VAL 3.4 0.2 + - - -
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Residues in contact with HIS 293 (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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69A LYS* 3.5 51.2 + - + +
70A ASN* 3.0 39.7 + - - +
72A MET* 3.6 7.1 - - - +
259A ASP* 2.9 30.2 + - + -
260A LEU 4.0 3.8 - - - -
261A PHE* 3.5 37.6 - + + -
291A PHE 4.2 0.2 + - - -
292A GLN* 1.3 72.2 - - - +
294A VAL* 1.3 60.3 + - - +
295A GLY* 3.3 14.7 + - - -
296A THR* 4.2 1.3 - - + -
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.9 5.2 - - + -
68A VAL* 3.7 2.0 - - + -
69A LYS* 2.8 23.0 + - - -
70A ASN 3.1 11.4 + - - +
72A MET* 3.9 20.0 - - + -
81A LEU* 3.7 31.0 - - + -
203A TRP* 4.8 4.5 - - + -
215A LEU* 5.3 0.2 - - + -
260A LEU* 2.7 42.1 + - + +
261A PHE 4.3 2.2 - - - -
262A VAL* 3.9 25.4 - - + +
292A GLN 3.8 9.0 - - - +
293A HIS* 1.3 77.0 - - - +
295A GLY* 1.3 57.4 - - - +
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Residues in contact with GLY 295 (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* 3.7 12.8 - - - -
67A LYS 3.2 14.4 - - - -
69A LYS* 3.8 5.6 - - - -
259A ASP* 3.4 0.7 - - - -
260A LEU 2.8 25.5 + - - -
293A HIS* 3.3 18.0 + - - -
294A VAL* 1.3 82.0 - - - +
296A THR* 1.3 60.0 + - - -
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Residues in contact with THR 296 (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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65A VAL 4.0 1.2 - - - +
66A PHE* 3.6 7.3 - - - -
67A LYS* 3.0 39.1 + - + +
69A LYS* 5.1 10.3 - - + +
257A GLU* 4.5 10.0 + - - +
258A TRP 3.2 9.4 + - - -
259A ASP* 3.2 23.8 - - - +
293A HIS* 4.2 7.9 - - + +
295A GLY* 1.3 78.1 - - - -
297A MET* 1.3 65.9 + - - +
298A THR* 4.0 8.1 + - - -
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Residues in contact with MET 297 (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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65A VAL 3.5 9.2 - - - +
66A PHE* 3.9 7.1 - - + -
90A VAL* 4.0 7.9 - - + -
92A ALA* 4.5 0.4 - - - -
94A PHE* 4.6 4.5 - - + -
113A PHE* 3.9 18.4 - - + -
115A VAL* 3.7 42.4 - - + -
217A TRP* 3.5 23.7 - - + -
256A PRO 3.9 0.3 - - - +
257A GLU* 3.0 8.3 - - - +
258A TRP* 2.8 59.7 + - + +
296A THR* 1.3 73.8 - - - +
298A THR* 1.3 63.6 + - - +
299A LEU* 3.7 28.0 - - + +
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Residues in contact with THR 298 (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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64A GLY* 3.1 3.1 - - - -
65A VAL* 3.0 44.9 + - + +
255A PHE* 3.8 32.5 - - + -
256A PRO 3.6 2.9 - - - -
257A GLU* 2.6 32.8 + - + +
296A THR* 4.0 6.5 + - - -
297A MET* 1.3 71.5 - - - +
299A LEU* 1.3 62.1 + - - +
300A ASN* 3.7 11.6 + - + +
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Residues in contact with LEU 299 (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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62A ALA* 4.1 17.0 - - + +
63A HIS 3.5 9.2 - - - +
64A GLY* 4.1 13.9 - - - +
90A VAL* 4.2 3.1 - - + -
92A ALA* 4.0 13.7 - - + -
94A PHE* 3.6 33.4 - - + -
246A THR* 5.9 1.3 - - + -
250A ILE* 3.5 17.9 - - + +
255A PHE* 3.5 6.7 - - - +
256A PRO* 3.0 37.9 + - + +
258A TRP* 3.7 18.8 - - + -
297A MET* 3.7 28.9 - - + +
298A THR* 1.3 71.3 - - - +
300A ASN* 1.3 59.0 + - - +
301A LYS 3.8 0.9 - - - -
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Residues in contact with ASN 300 (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* 3.1 1.6 + - - +
64A GLY* 3.7 15.7 - - - -
65A VAL* 4.3 20.0 - - - +
250A ILE* 3.6 8.2 - - - +
255A PHE* 3.5 45.5 - - + -
298A THR* 4.3 8.7 - - + +
299A LEU* 1.3 74.1 - - - +
301A LYS* 1.3 66.5 + - - +
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Residues in contact with LYS 301 (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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62A ALA* 3.8 2.1 - - - +
63A HIS* 3.0 49.5 + - + +
250A ILE* 3.6 6.0 - - - +
300A ASN* 1.3 89.0 - - - +
302A ASN* 1.3 71.0 + - - +
304A ASP* 3.6 28.6 + - - -
154B ARG* 6.0 0.8 - - - +
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Residues in contact with ASN 302 (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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60A PHE* 3.6 19.8 - - - -
61A GLY 4.9 0.3 - - - +
62A ALA* 4.6 3.3 - - - +
63A HIS* 4.1 3.8 - - - -
247A PHE* 3.0 60.0 + - + -
250A ILE* 3.7 14.9 - - - +
251A GLU* 2.8 34.9 + - - +
301A LYS* 1.3 95.4 + - - +
303A VAL* 1.3 66.0 + - - +
304A ASP 3.7 0.5 + - - -
154B ARG* 3.8 11.3 + - - +
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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