Contacts of the strand formed by residues 391 - 396 (chain A) in PDB entry 1PCU
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 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A CYS* 3.5 0.7 - - - -
346A ALA 2.9 37.9 + - - -
354A ASP* 2.9 24.3 + - - -
355A ALA* 4.0 16.2 - - - -
378A VAL* 6.2 0.4 - - - -
380A TRP 4.0 0.9 - - - -
390A TYR* 1.3 70.0 - - - +
392A VAL* 1.3 60.3 + - - -
393A TYR* 3.1 17.1 - - - -
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Residues in contact with VAL 392 (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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335A MET* 4.5 7.2 - - + -
339A VAL* 4.3 5.8 - - + -
343A MET* 3.7 41.7 - - + -
344A LEU 3.7 2.9 - - - +
345A CYS* 4.0 20.4 - - - +
355A ALA* 5.4 0.2 - - - +
378A VAL* 4.5 1.1 - - - +
379A SER* 3.0 28.8 + - - -
380A TRP* 2.9 57.7 + - + +
390A TYR 4.1 7.2 - - - +
391A GLY* 1.3 73.9 - - - -
393A TYR* 1.3 61.9 + - - +
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Residues in contact with TYR 393 (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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170A LEU* 4.5 6.2 - - - +
297A VAL* 3.6 13.9 - - + +
323A ILE* 3.3 29.4 - - + +
342A ASN 3.4 1.7 - - - +
343A MET* 3.5 2.4 - - - -
344A LEU* 2.8 51.6 + - + +
346A ALA* 3.8 5.6 - - + -
354A ASP* 4.7 0.9 + - - -
355A ALA* 4.6 2.9 - - - +
364A MET* 3.6 51.6 - - + -
375A VAL* 5.9 0.9 - - + -
376A GLY* 4.8 3.8 - - - +
377A LEU 3.3 17.9 - - - +
378A VAL* 3.7 28.8 - - + +
379A SER* 4.7 0.4 - - - -
391A GLY* 3.1 38.9 - - - -
392A VAL* 1.3 73.5 - - - +
394A THR* 1.3 63.5 + - - +
395A LYS* 3.3 3.1 + - - -
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Residues in contact with THR 394 (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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209A ALA* 5.0 1.8 - - + -
254A THR 5.8 0.4 - - - -
257A ASP* 2.6 50.2 + - - +
342A ASN* 3.6 6.9 - - - +
343A MET* 5.0 3.6 - - - +
376A GLY* 3.2 2.3 - - - -
377A LEU* 3.0 58.9 + - + +
379A SER* 4.0 11.7 - - - -
393A TYR* 1.3 67.2 - - - +
395A LYS* 1.3 61.6 + - - +
396A VAL* 3.4 5.0 + - - +
399A TYR* 2.6 24.5 + - + -
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Residues in contact with LYS 395 (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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288A LEU* 4.4 13.3 - - + +
328A HIS* 3.9 26.3 - - - -
341A GLU 5.0 1.6 - - - -
342A ASN 2.9 19.0 + - - +
344A LEU* 4.1 31.2 - - + +
375A VAL* 3.6 17.9 - - + +
376A GLY* 4.1 1.6 - - - -
393A TYR 3.3 5.3 + - - +
394A THR* 1.3 68.7 + - - +
396A VAL* 1.3 56.9 + - - +
397A SER* 3.2 27.1 - - - +
398A ARG* 3.2 43.6 + - + +
399A TYR* 3.1 19.0 - - - -
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Residues in contact with VAL 396 (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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207A LEU* 4.3 2.9 - - + -
258A ILE* 3.9 22.7 - - + -
278A LEU* 5.0 1.6 - - + -
279A PRO* 3.8 24.7 - - + +
374A LEU* 3.7 31.0 - - + +
375A VAL 2.9 11.3 + - - +
376A GLY* 4.2 2.7 - - - -
377A LEU* 4.2 8.5 - - + -
394A THR 4.1 8.5 - - - +
395A LYS* 1.3 69.0 - - - +
397A SER* 1.3 60.7 + - - +
399A TYR* 3.4 15.9 + - + -
400A LEU* 3.7 10.6 + - - +
403A ILE* 3.7 29.9 - - + +
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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