Contacts of the strand formed by residues 325 - 332 (chain A) in PDB entry 1IGR
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 ILE 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A PRO* 6.5 0.9 - - + -
300A LYS 3.0 2.5 + - - +
301A VAL* 4.0 34.8 - - + -
302A CYS* 2.7 34.5 + - - +
323A CYS* 3.6 2.7 - - - +
324A THR* 1.3 92.6 - - - +
326A PHE* 1.3 65.9 - - - +
327A LYS* 5.2 0.4 - - + -
351A ILE* 5.2 0.2 - - - -
353A VAL* 3.4 35.2 - - + +
355A THR* 4.3 11.4 - - + -
376A ARG* 6.2 0.2 - - - +
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Residues in contact with PHE 326 (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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302A CYS* 3.7 20.2 - - + -
304A GLU* 3.7 29.4 - - + -
306A LYS 5.6 1.3 - - - -
307A LYS 4.3 2.5 - - - -
309A LYS* 3.5 23.3 - - + -
320A LEU* 3.9 24.0 - - + -
323A CYS* 5.5 1.8 - - + -
324A THR 4.3 0.2 - - - -
325A ILE* 1.3 73.5 - - - +
327A LYS* 1.3 61.6 + - - +
328A GLY* 3.3 16.6 + - - -
329A ASN 3.6 30.7 - - - -
330A LEU* 4.1 20.0 - - + -
351A ILE* 4.6 14.5 - - + +
353A VAL 2.8 14.4 + - - +
354A VAL* 3.6 12.8 - - + -
355A THR* 2.9 26.9 + - - +
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Residues in contact with LYS 327 (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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301A VAL* 4.5 14.6 - - + -
302A CYS 2.9 15.2 + - - +
303A GLU* 3.9 29.2 - - + +
304A GLU 4.6 1.4 + - - -
306A LYS 5.6 1.4 - - - +
307A LYS* 4.8 0.7 - - - +
325A ILE* 3.8 2.9 - - + +
326A PHE* 1.3 74.4 - - - +
328A GLY* 1.3 59.2 + - - +
355A THR* 3.3 29.6 - - + -
381A GLU* 5.1 6.5 - - - -
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Residues in contact with GLY 328 (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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307A LYS* 3.2 19.5 - - - -
326A PHE* 3.3 9.5 + - - -
327A LYS* 1.3 77.0 - - - +
329A ASN* 1.3 67.5 + - - +
354A VAL* 3.8 7.1 - - - +
355A THR* 3.0 7.6 + - - -
356A GLY* 2.9 25.5 + - - -
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Residues in contact with ASN 329 (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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307A LYS* 2.7 16.0 + - - +
308A THR* 3.2 29.1 + - + +
309A LYS* 2.5 36.2 + - - +
326A PHE* 3.6 7.6 - - - -
328A GLY* 1.3 75.4 - - - +
330A LEU* 1.3 57.3 + - - +
331A LEU 4.0 0.2 - - - -
354A VAL* 4.9 0.4 - - - -
356A GLY* 2.9 33.6 - - - -
357A TYR* 2.9 43.0 + - + +
382A GLU* 3.4 25.9 + - - +
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Residues in contact with LEU 330 (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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308A THR* 4.6 1.1 - - - -
309A LYS* 3.5 7.4 - - + -
311A ILE* 3.9 11.2 - - + -
320A LEU* 3.7 27.1 - - + -
326A PHE* 4.1 24.2 - - + -
329A ASN* 1.3 72.9 - - - +
331A LEU* 1.3 59.5 + - - +
332A ILE* 3.8 11.7 - - + -
348A MET* 4.6 7.2 - - + -
351A ILE* 4.8 6.5 - - + -
354A VAL* 3.8 26.6 - - + +
357A TYR* 3.3 8.8 + - - +
358A VAL* 3.5 17.0 - - + +
359A LYS* 2.8 27.5 + - - +
372A LEU* 4.5 20.6 - - + -
375A LEU* 6.5 0.2 - - + -
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Residues in contact with LEU 331 (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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308A THR* 3.8 20.2 - - + -
309A LYS 2.9 10.0 + - - +
310A THR* 3.3 25.2 - - + +
311A ILE 3.0 23.4 + - - -
329A ASN 3.9 0.6 + - - -
330A LEU* 1.3 72.3 - - - +
332A ILE* 1.3 59.2 + - - +
333A ASN* 3.6 9.6 + - + -
357A TYR* 5.9 1.1 - - + -
359A LYS* 3.3 35.7 - - + +
361A ARG* 4.0 37.7 - - + +
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Residues in contact with ILE 332 (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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311A ILE* 3.7 25.1 - - + +
330A LEU* 3.8 9.2 - - + -
331A LEU* 1.3 73.7 - - - +
333A ASN* 1.3 60.9 + - - +
334A ILE* 3.6 29.6 - - + -
348A MET* 4.2 18.2 - - + -
358A VAL* 4.3 13.2 - - + -
359A LYS 2.6 10.7 + - - -
360A ILE* 3.4 30.1 - - + -
361A ARG 3.1 22.9 + - - -
363A SER* 3.2 10.0 + - - +
366A LEU* 4.2 11.2 - - + -
371A PHE* 4.6 8.5 - - + -
372A LEU* 4.4 11.0 - - + -
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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