Contacts of the strand formed by residues 434 - 442 (chain A) in PDB entry 2V5Y
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 ASN 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A CYS 3.3 11.8 - - - +
401A TYR* 3.6 9.0 - - - +
402A GLN* 5.8 1.0 + - - -
433A THR* 1.3 73.0 - - - +
435A VAL* 1.3 62.2 + - - +
436A SER* 3.6 1.7 + - - -
454A ILE* 4.2 17.9 - - + +
455A VAL 3.9 3.6 - - - -
456A GLN* 3.4 23.0 + - - +
1573A NAG 1.4 67.2 + - - +
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Residues in contact with VAL 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 4.8 9.4 - - + -
399A TYR* 3.6 22.0 - - + -
400A CYS 3.5 5.8 - - - +
401A TYR* 4.4 9.2 - - + -
426A ILE* 5.1 1.8 - - + -
429A LEU* 3.9 24.7 - - + -
433A THR* 4.0 2.0 - - - +
434A ASN* 1.3 72.5 - - - +
436A SER* 1.3 62.4 + - - +
437A VAL* 3.5 25.3 + - + +
454A ILE* 3.4 2.8 - - - -
455A VAL 2.9 38.9 + - - +
457A THR* 3.5 30.5 - - + -
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Residues in contact with SER 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A HIS* 3.4 2.9 - - - +
399A TYR* 3.1 5.0 - - - -
400A CYS* 3.0 44.8 + - - +
434A ASN 3.6 2.1 + - - -
435A VAL* 1.3 71.4 - - - +
437A VAL* 1.3 58.8 + - - +
438A LYS* 6.0 0.2 - - - +
452A GLU* 3.2 35.3 + - - +
453A LEU 3.5 5.4 + - - -
454A ILE* 4.1 11.0 - - - +
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Residues in contact with VAL 437 (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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366A LEU* 4.4 5.6 - - + +
376A ILE* 4.5 10.5 - - + -
378A ILE* 3.5 33.9 - - + -
397A VAL* 4.0 13.9 - - + -
398A HIS 3.5 5.4 - - - +
399A TYR* 4.2 1.1 - - + -
426A ILE* 4.1 13.0 - - + -
435A VAL* 3.5 31.6 - - + +
436A SER* 1.3 72.8 - - - +
438A LYS* 1.3 69.0 + - - +
451A GLN 4.2 0.3 - - - +
452A GLU* 3.7 2.8 - - - +
453A LEU* 2.8 43.6 + - + +
455A VAL* 4.7 6.1 - - + -
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Residues in contact with LYS 438 (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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366A LEU* 4.4 1.8 - - - -
397A VAL* 3.7 1.4 - - - -
398A HIS* 2.8 78.1 + - + +
437A VAL* 1.3 81.1 - - - +
439A LEU* 1.3 62.6 + - - +
440A ILE* 3.9 19.1 - - + -
449A GLU* 2.6 43.5 + - + +
450A SER* 4.1 11.0 - - - +
451A GLN 4.3 2.9 - - - +
452A GLU* 3.7 28.7 + - + +
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Residues in contact with LEU 439 (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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363A PRO* 3.9 22.5 - - + +
366A LEU* 3.9 22.0 - - + -
378A ILE* 4.5 3.1 - - + -
380A TRP* 3.6 56.5 - - + -
395A LEU* 4.3 9.2 - - + -
396A THR 3.4 4.9 - - - +
397A VAL* 3.8 37.0 - - + -
438A LYS* 1.3 72.0 - - - +
440A ILE* 1.3 62.0 + - - +
441A LEU 3.8 1.4 + - - -
449A GLU* 3.5 1.0 - - - -
450A SER* 2.8 43.0 + - - +
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Residues in contact with ILE 440 (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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395A LEU* 3.9 2.3 - - - -
396A THR* 2.8 42.6 + - + +
398A HIS* 3.9 20.9 - - + +
411A GLU* 3.5 24.7 - - - +
438A LYS* 3.9 20.9 - - + -
439A LEU* 1.3 73.7 - - - +
441A LEU* 1.3 59.9 + - - +
442A MET* 3.9 6.8 + - + +
447A ARG* 3.3 48.5 - - + +
448A LYS 4.1 2.2 - - - -
449A GLU* 4.1 14.6 - - + +
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Residues in contact with LEU 441 (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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359A PRO* 4.1 18.6 - - + +
361A ARG 3.8 9.0 - - - +
363A PRO* 4.3 7.9 - - + -
383A PHE* 3.8 26.7 - - + -
387A VAL* 3.7 30.3 - - + -
388A THR* 4.3 7.9 - - + -
393A TYR* 4.2 13.0 - - + -
394A ASN 3.5 15.7 - - - +
395A LEU* 4.1 12.6 - - + -
439A LEU 3.8 1.4 + - - -
440A ILE* 1.3 71.9 - - - +
442A MET* 1.3 68.9 + - - +
443A ASN* 6.3 0.2 - - + -
447A ARG* 3.2 6.8 - - - +
448A LYS 3.1 38.8 + - - +
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Residues in contact with MET 442 (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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359A PRO* 4.9 0.7 - - - -
393A TYR* 3.2 7.7 - - - +
394A ASN* 3.0 47.1 + - - +
396A THR* 5.5 3.8 - - - +
440A ILE* 4.3 6.7 - - + +
441A LEU* 1.3 78.7 - - - +
443A ASN* 1.3 68.8 + - - +
446A GLY 3.9 4.0 - - - +
447A ARG* 3.2 52.0 - - + +
1574A NAG 3.7 50.8 - - + +
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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