Contacts of the strand formed by residues 286 - 293 (chain A) in PDB entry 5IQL
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 PRO 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A PHE 4.4 2.6 - - - +
258A LEU 5.6 0.3 - - - -
259A HIS* 5.4 1.0 + - + -
285A PHE* 1.3 97.4 - - + +
287A VAL* 1.3 63.2 + - - +
288A ARG* 3.7 2.6 + - - +
304A ILE* 3.6 24.7 - - + -
305A HIS 3.4 7.0 - - - +
306A ASN* 3.9 13.9 - - - +
26B ARG 4.0 9.9 - - - +
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Residues in contact with VAL 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A TRP* 5.3 0.9 - - + -
236A VAL* 4.3 14.6 - - + -
256A PHE* 4.3 12.6 - - + -
257A PHE 4.1 4.5 - - - +
258A LEU* 4.2 19.1 - - + -
277A LEU* 5.8 0.2 - - + -
285A PHE* 3.8 27.8 - - + +
286A PRO* 1.3 70.8 - - - +
288A ARG* 1.3 63.7 + - - +
289A VAL* 3.7 18.2 + - + +
303A ILE 3.6 1.0 - - - +
304A ILE* 3.4 2.6 - - - -
305A HIS* 2.6 52.4 + - + +
307A LEU* 4.2 21.8 - - + -
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Residues in contact with ARG 288 (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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256A PHE* 3.6 2.8 - - - -
257A PHE* 2.8 83.2 + - + +
286A PRO 3.7 3.6 + - - +
287A VAL* 1.3 71.8 - - - +
289A VAL* 1.3 65.8 + - - +
290A GLN* 3.3 24.5 + - - -
302A ASP* 3.6 27.3 + - - -
303A ILE 3.6 3.8 - - - +
304A ILE* 4.6 18.2 - - + +
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Residues in contact with VAL 289 (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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212A VAL* 3.8 30.1 - - + -
236A VAL* 4.7 0.2 - - + -
238A VAL* 3.8 11.7 - - + -
254A VAL* 3.5 24.7 - - + -
255A TRP 3.4 3.1 - - - -
256A PHE* 4.0 21.8 - - + -
287A VAL* 4.2 11.2 - - + +
288A ARG* 1.3 76.8 - - - +
290A GLN* 1.3 62.5 + - - +
291A VAL* 3.9 15.5 - - + -
301A ILE 3.6 0.9 - - - +
302A ASP* 3.4 3.8 - - - +
303A ILE* 2.7 50.2 + - + +
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Residues in contact with GLN 290 (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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254A VAL* 3.3 4.0 - - - -
255A TRP* 2.8 46.6 + - + +
257A PHE* 4.0 24.4 - - + -
288A ARG* 3.3 14.9 + - - -
289A VAL* 1.3 73.4 - - - +
291A VAL* 1.3 62.0 - - - +
292A HIS* 2.8 36.1 + - + +
300A ARG* 3.5 31.5 + - + +
301A ILE 3.4 4.7 - - - +
302A ASP* 2.9 24.6 - - - +
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Residues in contact with VAL 291 (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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210A ILE* 4.0 9.0 - - + -
238A VAL* 4.2 17.3 - - + -
251A VAL* 3.8 34.5 - - + -
253A LYS 3.8 2.9 - - - -
254A VAL* 4.2 3.8 - - + -
289A VAL* 3.9 20.2 - - + -
290A GLN* 1.3 75.3 - - - +
292A HIS* 1.3 62.0 + - - +
293A PHE* 3.9 20.4 - - + -
300A ARG* 3.3 5.9 - - - -
301A ILE* 2.9 37.9 + - + +
303A ILE* 4.5 16.4 - - + -
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Residues in contact with HIS 292 (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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251A VAL* 3.5 6.1 - - - +
252A LYS* 2.7 33.1 + - + +
253A LYS* 2.8 44.9 + - + +
255A TRP* 3.2 28.1 - + - -
290A GLN* 2.8 42.9 + - + +
291A VAL* 1.3 74.4 - - - +
293A PHE* 1.3 58.0 + - - +
300A ARG* 3.6 24.8 - - + +
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Residues in contact with PHE 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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210A ILE* 4.2 7.2 - - + -
250A PHE* 3.3 39.0 - + + +
251A VAL* 4.4 1.3 - - + -
252A LYS* 3.8 12.4 + - - +
291A VAL* 3.9 32.1 - - + -
292A HIS* 1.3 79.3 - - - +
294A LYS* 1.3 68.2 + - - +
295A ASP 3.3 9.5 - - - +
296A SER* 3.9 5.7 + - - -
298A ASN* 3.7 37.3 + - + +
299A LYS 3.4 26.5 - - - -
300A ARG* 5.3 0.4 - - - +
301A ILE* 4.0 19.5 - - + -
327A VAL* 4.3 15.9 - - + -
328A GLU 5.7 0.9 - - - -
329A LEU* 4.0 12.6 - - + -
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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