Contacts of the strand formed by residues 413 - 422 (chain A) in PDB entry 3GVJ
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 LEU 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A GLU* 3.6 24.5 - - + -
405A THR 3.6 10.3 - - - +
406A ARG* 3.7 21.9 - - - +
411A ASN 3.6 3.0 + - - -
412A ALA* 1.3 74.8 - - - +
414A THR* 1.3 59.4 + - - +
415A ASN 3.4 25.1 - - - +
416A CYS* 3.9 17.9 - - - -
519A LEU* 3.6 29.6 - - + +
523A VAL* 3.5 35.9 - - + +
524A THR* 3.9 10.3 - - - +
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Residues in contact with THR 414 (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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385A VAL* 4.3 10.1 - - + +
405A THR* 2.8 23.6 + - + -
407A THR* 3.9 16.3 - - - +
412A ALA* 3.6 9.2 + - - +
413A LEU* 1.3 75.6 + - - +
415A ASN* 1.3 59.9 + - + +
519A LEU* 3.6 26.0 + - + +
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Residues in contact with ASN 415 (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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403A ILE 4.8 0.5 - - - +
404A GLU* 3.4 0.7 - - - -
405A THR* 3.0 44.3 + - + +
413A LEU* 3.4 10.5 - - - +
414A THR* 1.3 81.5 + - + +
416A CYS* 1.3 73.1 + - - +
417A ALA* 4.0 10.0 + - - +
516A ASP* 2.8 31.4 + - - +
518A GLY* 3.6 19.7 - - - -
519A LEU* 4.3 1.1 - - - +
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Residues in contact with CYS 416 (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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402A MET* 4.0 10.3 - - - -
403A ILE 4.1 2.7 - - - -
404A GLU* 4.7 8.3 - - - +
413A LEU* 3.9 26.7 - - - -
415A ASN* 1.3 80.9 - - - +
417A ALA* 1.3 60.8 - - - +
517A LEU* 2.8 27.3 + - + +
518A GLY 2.8 17.2 + - - +
519A LEU* 5.2 0.2 - - - -
520A ILE* 3.6 40.4 - - + -
523A VAL* 5.0 0.7 - - - -
526A VAL* 4.7 10.8 - - - -
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Residues in contact with ALA 417 (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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401A ALA 3.6 0.3 - - - +
402A MET* 3.7 6.9 - - - +
403A ILE* 2.9 37.9 + - - +
415A ASN* 4.0 10.1 - - - +
416A CYS* 1.3 76.4 - - - +
418A LEU* 1.3 60.8 + - - +
419A TRP* 3.6 25.4 + - + +
514A LYS* 5.4 1.1 - - + -
515A THR 3.4 15.0 - - - +
516A ASP* 4.4 3.4 - - - -
517A LEU 4.3 0.4 - - - +
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PHE* 4.0 26.7 - - + -
401A ALA 3.6 9.2 - - - +
402A MET* 4.5 2.5 - - - -
417A ALA* 1.3 72.0 - - - +
419A TRP* 1.3 60.1 + - - +
420A ASP* 4.6 4.0 - - - +
513A ARG 3.6 1.4 - - - +
514A LYS* 3.6 0.9 - - - -
515A THR* 2.9 40.2 + - - +
517A LEU* 4.1 14.8 - - + +
537A PHE* 4.0 15.9 - - + -
539A MET* 3.8 33.2 - - + -
556A PHE* 4.5 9.4 - - + -
559A ALA* 5.0 0.9 - - + -
563A PRO* 3.9 35.9 - - + +
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Residues in contact with TRP 419 (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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375A LEU 4.9 1.3 - - - -
376A THR* 4.2 19.1 - - + -
377A ASP 6.2 0.2 - - - -
387A TYR* 4.0 33.7 - + - -
399A LEU 3.8 0.3 - - - +
400A PHE* 3.5 0.9 - - - -
401A ALA* 2.9 33.9 + - + +
403A ILE* 3.5 37.8 - - + +
417A ALA* 3.6 26.9 - - + +
418A LEU* 1.3 82.1 - - - +
420A ASP* 1.3 62.1 + - - +
512A TRP* 3.6 45.1 - + + -
513A ARG 3.3 4.5 - - - +
514A LYS* 3.5 49.6 - - + +
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Residues in contact with ASP 420 (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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398A ARG* 2.8 38.1 + - - +
399A LEU 3.0 17.0 - - - +
400A PHE* 3.5 22.7 - - + -
418A LEU* 4.6 6.8 - - - +
419A TRP* 1.3 76.2 - - - +
421A ARG* 1.3 60.9 + - - +
512A TRP* 3.4 7.5 - - - -
513A ARG* 2.9 77.5 + - - +
515A THR* 5.1 0.9 + - - -
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Residues in contact with ARG 421 (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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375A LEU* 5.3 1.4 + - - +
398A ARG* 3.3 7.1 - - - +
399A LEU* 2.8 29.9 + - - +
420A ASP* 1.3 75.4 - - - +
422A PRO* 1.3 75.4 - - + +
507A PHE* 3.0 60.2 + - + +
508A HIS* 3.4 19.0 + - - +
510A SER 2.9 23.4 + - - +
511A PRO* 3.9 11.8 - - - +
512A TRP* 3.3 49.1 - - + +
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Residues in contact with PRO 422 (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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397A ASN 3.8 9.4 - - - +
398A ARG* 3.5 25.4 - - + +
421A ARG* 1.3 93.7 - - + +
423A MET* 1.3 63.9 + - - +
449A HIS 5.9 0.2 - - - +
450A GLY 4.6 2.0 - - - +
451A LEU* 4.0 19.7 - - + -
455A ASP* 3.8 11.0 - - + +
505A THR* 5.3 2.0 - - - -
506A SER 4.1 4.7 - - - +
507A PHE* 3.1 28.7 + - - +
510A SER* 3.5 32.3 - - - +
511A PRO 4.5 0.9 - - - +
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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