Contacts of the strand formed by residues 370 - 378 (chain D) in PDB entry 2Y1X
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 ARG 370 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366D GLY 4.5 1.4 + - - -
367D ASP 3.9 8.9 + - - +
369D HIS* 1.3 82.6 - - + +
371D ILE* 1.3 61.5 + - - +
372D GLU* 2.7 44.1 + - - +
440D LEU* 4.0 30.2 - - + +
441D LEU 3.5 5.4 - - - +
442D ILE* 4.8 8.1 - - + +
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Residues in contact with ILE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D PHE* 3.6 44.2 - - + -
356D TYR* 3.8 31.4 - - + +
367D ASP 4.1 4.5 - - - +
368D LEU* 3.9 22.7 - - + +
370D ARG* 1.3 74.7 - - - +
372D GLU* 1.3 59.3 + - - +
373D ILE* 3.8 19.1 - - + -
439D CYS 3.7 2.3 - - - +
440D LEU* 3.4 4.8 - - - +
441D LEU* 2.8 48.7 + - + +
449D TYR* 3.8 19.1 - - + +
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Residues in contact with GLU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D TYR* 3.7 15.6 + - - -
370D ARG* 2.7 48.9 + - - +
371D ILE* 1.3 73.2 - - - +
373D ILE* 1.3 62.4 + - - +
374D PRO* 3.5 18.9 - - + +
438D THR* 3.9 27.4 + - + +
440D LEU* 3.9 8.7 - - + -
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Residues in contact with ILE 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D PHE* 5.2 0.9 - - + -
293D VAL* 5.1 8.3 - - + -
295D LEU* 4.2 32.5 - - + -
354D VAL* 4.9 7.6 - - + -
355D LYS 5.4 0.4 - - - +
356D TYR* 3.8 41.1 - - + -
371D ILE* 3.8 17.7 - - + +
372D GLU* 1.3 76.7 - - - +
374D PRO* 1.3 72.5 - - + +
375D PHE* 3.7 3.3 - - - -
390D PHE* 5.6 0.9 - - + -
438D THR* 3.7 2.6 - - - -
439D CYS* 2.9 46.9 + - + +
441D LEU* 4.4 15.0 - - + -
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Residues in contact with PRO 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D VAL* 4.0 9.0 - - - +
356D TYR* 5.3 3.8 - - + -
372D GLU* 3.5 18.3 - - + +
373D ILE* 1.3 94.3 - - + +
375D PHE* 1.3 61.5 + - - +
437D GLY 3.6 8.5 - - - +
438D THR* 4.5 7.9 - - - +
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Residues in contact with PHE 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 4.2 13.7 - - + -
354D VAL* 4.2 11.7 - - + -
373D ILE 3.7 10.8 - - - -
374D PRO* 1.3 74.7 - - - +
376D LYS* 1.3 60.9 + - - +
377D PHE* 3.5 39.0 - + + -
388D LEU* 3.9 22.9 - - + -
435D LEU* 3.9 7.4 - - + -
436D SER* 3.3 13.5 - - - -
437D GLY 3.0 38.4 + - - +
438D THR 3.4 24.2 - - - -
439D CYS* 3.5 2.7 - - + -
453D ILE* 4.6 0.9 - - + -
454D VAL 3.3 20.9 - - - -
455D ALA* 4.1 12.1 - - + -
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Residues in contact with LYS 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D VAL* 4.0 13.4 - - - +
375D PHE* 1.3 74.5 - - - +
377D PHE* 1.3 64.1 + - - +
378D HIS* 4.1 16.6 + - + +
434D THR* 4.2 23.6 - - + -
435D LEU 3.6 2.0 - - - -
436D SER* 4.3 11.4 - - - -
458D ASP* 3.5 23.0 + - - -
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Residues in contact with PHE 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D LEU* 3.3 37.7 - - + -
296D ALA* 3.8 0.7 - - - -
297D PRO* 3.6 31.2 - - + -
351D ALA* 3.8 11.9 - - + -
352D LYS 3.4 21.5 - - - -
354D VAL* 3.4 27.4 - - + -
375D PHE* 3.5 35.7 - + + -
376D LYS* 1.3 73.3 - - - +
378D HIS* 1.3 62.7 + - - +
379D MET* 3.8 4.8 + - + -
388D LEU* 4.2 13.0 - - + -
433D ASP 3.8 0.2 - - - +
434D THR* 3.1 8.4 - - - -
435D LEU* 2.8 45.1 + - + +
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Residues in contact with HIS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D ALA* 3.2 17.9 - - - +
352D LYS 4.6 0.9 + - - -
376D LYS* 4.7 18.1 - - + +
377D PHE* 1.3 75.0 - - - +
379D MET* 1.3 63.9 + - - +
380D LEU* 3.4 9.9 + - + +
432D GLY* 4.8 6.5 + - - +
433D ASP 3.6 5.1 + - - +
434D THR* 3.1 27.2 - - + +
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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