Contacts of the strand formed by residues 316 - 322 (chain A) in PDB entry 3IQL
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 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A CYS* 4.3 10.5 - - + -
295A CYS 3.5 6.7 - - - +
296A ARG* 3.9 27.6 - - + +
314A GLY 3.7 14.6 - - - +
315A ASP* 1.3 72.9 - - - +
317A ILE* 1.3 63.1 + - - +
318A THR* 4.0 1.7 + - - -
332A LEU* 3.4 17.0 - - - +
347A LEU* 4.0 12.3 - - + -
286B ALA* 3.7 24.9 - - + +
287B SER 3.4 33.7 - - - +
288B VAL* 4.0 7.7 - - - +
289B GLY* 4.6 10.9 + - - +
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Residues in contact with ILE 317 (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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294A CYS* 3.2 5.7 - - - +
295A CYS* 2.8 38.1 + - - -
297A ALA* 4.1 12.8 - - + +
309A LEU* 4.1 8.3 - - + -
311A PHE* 3.5 43.3 - - + -
315A ASP 4.2 2.5 - - - +
316A ILE* 1.3 75.6 - - - +
318A THR* 1.3 75.5 + - - +
319A LEU 3.4 0.2 + - - -
331A MET 3.6 10.5 - - - +
332A LEU* 4.5 14.4 - - + -
339A PHE* 3.7 27.4 - - + -
344A VAL* 4.0 19.5 - - + -
288B VAL* 5.5 0.2 - - - -
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Residues in contact with THR 318 (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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292A GLN* 3.5 34.1 - - + +
293A PRO 3.9 3.1 - - - -
294A CYS* 4.3 2.9 - - - -
316A ILE 4.0 1.9 + - - -
317A ILE* 1.3 73.2 - - - +
319A LEU* 1.3 56.9 + - - +
320A THR* 4.4 8.3 - - + -
330A GLY* 3.0 6.2 - - - -
331A MET* 2.8 41.7 + - + -
288B VAL* 3.8 16.4 - - - +
289B GLY 5.3 0.7 + - - -
292B GLN* 2.7 38.1 + - - +
318B THR* 4.1 5.4 - - + -
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Residues in contact with LEU 319 (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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292A GLN* 3.1 20.4 + - - -
293A PRO* 2.9 24.0 + - + +
294A CYS 3.8 16.4 - - - +
295A CYS* 3.8 12.6 - - + -
317A ILE 3.4 1.0 + - - -
318A THR* 1.3 72.7 - - - +
320A THR* 1.3 59.6 + - - +
321A ASN 4.8 0.9 - - - +
328A TYR* 3.6 42.0 - - + -
329A GLU 4.0 3.6 - - - +
339A PHE* 3.8 16.4 - - + -
346A ILE* 3.4 30.1 - - + -
348A VAL 3.9 9.4 - - - +
350A LEU* 4.3 16.4 - - + +
331B MET* 3.5 3.6 - - - +
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Residues in contact with THR 320 (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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318A THR* 4.1 8.5 - - + +
319A LEU* 1.3 78.6 - - - +
321A ASN* 1.3 69.2 + - - +
329A GLU* 2.9 36.7 + - - +
330A GLY* 3.5 12.2 + - - -
331A MET* 4.1 13.5 - - + -
350A LEU* 4.0 11.2 - - - +
320B THR* 3.7 30.1 - - + -
331B MET* 3.6 11.3 - - - +
336B SER* 4.1 14.7 + - - -
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Residues in contact with ASN 321 (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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319A LEU* 3.9 0.4 - - - +
320A THR* 1.3 80.9 + - - +
322A GLN* 1.3 83.3 + - - +
323A ILE* 4.2 7.4 - - + -
328A TYR* 3.4 9.5 - - - -
329A GLU* 2.8 49.3 + - + +
350A LEU* 3.6 13.1 - - - +
336B SER* 5.5 4.8 + - - -
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Residues in contact with GLN 322 (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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321A ASN* 1.3 88.4 + - - +
323A ILE* 1.3 62.0 + - - +
324A ASP* 2.9 29.9 + - - +
325A GLU* 4.2 4.9 - - - +
327A TRP 3.7 8.3 - - - +
328A TYR* 3.8 27.1 + - + -
341A ILE* 3.5 11.6 - - + +
350A LEU* 3.9 9.0 - - + +
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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