Contacts of the strand formed by residues 398 - 409 (chain A) in PDB entry 4TVJ
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 THR 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A GLN* 5.7 2.7 - - - -
390A HIS* 3.8 9.2 - - + +
395A SER 6.2 0.2 - - - +
397A TYR* 1.3 79.6 - - - +
399A MET* 1.3 63.7 + - - +
577A PHE* 3.5 4.2 - - - -
578A ASN* 2.7 55.9 + - - +
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Residues in contact with MET 399 (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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386A LEU* 3.7 25.8 - - + +
387A GLN* 2.9 29.4 + - - +
390A HIS* 3.5 24.8 + - + +
397A TYR* 3.6 15.9 - - + -
398A THR* 1.3 83.3 - - - +
400A THR* 1.3 63.6 + - - +
467A SER* 3.5 27.8 - - - +
468A SER* 4.2 8.5 - - - -
471A ALA* 3.6 24.0 - - + -
485A LEU* 4.1 2.5 - - - -
575A VAL* 3.7 24.7 - - + -
576A GLN 3.3 3.4 - - - -
577A PHE* 4.2 5.6 - - + -
578A ASN* 3.9 0.7 - - - -
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Residues in contact with THR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLN* 4.8 0.9 - - - +
399A MET* 1.3 72.6 + - - +
401A LEU* 1.3 71.3 + - - +
402A LEU* 3.3 14.4 + - + -
575A VAL* 3.4 4.4 - - - -
576A GLN* 2.7 50.1 + - - +
578A ASN* 2.8 26.2 + - - -
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Residues in contact with LEU 401 (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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374A HIS* 5.2 1.2 - - - -
379A PHE* 3.5 35.6 - - + -
382A ILE* 4.8 5.2 - - + -
383A SER* 3.3 36.6 - - - +
386A LEU* 3.9 16.0 - - + +
387A GLN* 5.0 2.1 - - - +
399A MET 4.2 1.0 + - - -
400A THR* 1.3 77.5 - - - +
402A LEU* 1.3 61.1 + - - +
403A ASP 3.5 22.7 - - - +
404A LEU* 4.8 2.5 - - + -
573A LEU* 3.6 38.8 - - + -
574A LYS 3.7 6.1 - - - +
575A VAL* 4.4 2.5 - - + +
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Residues in contact with LEU 402 (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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374A HIS* 3.3 17.4 - - - -
400A THR* 3.3 13.9 + - + -
401A LEU* 1.3 74.3 - - - +
403A ASP* 1.3 61.6 + - - +
482A THR* 4.5 10.5 - - - +
574A LYS* 2.7 41.3 + - + +
575A VAL 4.5 2.0 - - - -
576A GLN* 3.8 50.5 - - + +
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Residues in contact with ASP 403 (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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237A ARG* 2.8 58.7 + - - +
374A HIS* 2.9 16.2 + - - -
379A PHE* 4.8 0.9 - - - -
401A LEU* 3.5 10.5 - - - +
402A LEU* 1.3 80.4 - - - +
404A LEU* 1.3 69.7 + - - +
405A PHE* 4.0 20.3 - - + -
573A LEU* 3.6 0.2 - - - -
574A LYS* 2.9 37.7 + - + +
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Residues in contact with LEU 404 (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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371A PRO* 3.5 4.2 - - - +
372A LEU* 2.9 50.7 + - + +
374A HIS* 4.5 0.4 + - - -
379A PHE* 3.8 47.8 - - + +
382A ILE* 3.9 19.5 - - + -
401A LEU* 4.8 3.1 - - + -
403A ASP* 1.3 86.0 + - - +
405A PHE* 1.3 67.5 + - - +
571A TYR* 4.0 13.7 - - + -
572A LEU 3.6 5.6 - - - +
573A LEU* 3.8 33.7 - - + -
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Residues in contact with PHE 405 (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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237A ARG* 3.8 29.8 - - + -
238A VAL* 4.1 8.5 - - + -
241A LEU* 4.0 36.3 - - + -
369A LEU* 4.7 6.5 - - + -
370A ARG 3.3 8.3 - - - +
371A PRO* 3.7 33.2 - - + -
372A LEU* 4.6 0.7 - - - -
403A ASP* 4.0 33.2 - - + -
404A LEU* 1.3 75.8 - - - +
406A GLU* 1.3 67.6 + - - +
571A TYR* 3.2 10.8 - - - +
572A LEU* 2.9 52.5 + - + +
574A LYS* 4.7 10.5 - - + -
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Residues in contact with GLU 406 (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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368A ALA 3.6 0.9 - - - +
369A LEU* 3.3 8.0 - - - -
370A ARG* 2.7 77.0 + - + +
372A LEU* 4.1 25.3 - - + +
405A PHE* 1.3 75.1 - - - +
407A VAL* 1.3 66.5 + - - +
408A GLU* 4.4 2.3 - - + +
570A ARG* 3.5 28.7 + - - +
571A TYR* 4.3 3.4 - - - -
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Residues in contact with VAL 407 (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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367A CYS* 3.6 25.1 - - - -
368A ALA 3.5 3.4 - - - +
369A LEU* 4.2 8.7 - - + -
406A GLU* 1.3 81.9 - - - +
408A GLU* 1.3 64.1 + - - +
409A LYS 4.4 1.3 - - - +
439A LEU* 4.6 4.9 - - + -
486A LEU* 4.5 5.8 - - + -
568A ARG* 5.5 1.4 + - - -
569A MET* 3.1 38.7 - - + +
570A ARG* 2.8 28.6 + - - +
571A TYR 3.7 7.6 - - - +
572A LEU* 3.7 36.8 - - + +
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Residues in contact with GLU 408 (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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367A CYS* 3.5 1.1 - - - -
368A ALA* 2.8 40.3 + - + +
370A ARG* 3.0 39.4 + - - +
406A GLU* 4.4 2.3 - - + +
407A VAL* 1.3 74.4 - - - +
409A LYS* 1.3 66.0 + - - +
410A ASP* 3.6 4.6 + - - +
413A LYS* 4.8 16.9 - - + +
568A ARG* 4.7 17.3 - - - +
569A MET 4.8 0.9 - - - -
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Residues in contact with LYS 409 (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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365A LEU 3.0 11.3 + - - -
366A HIS* 2.9 26.8 + - - +
367A CYS* 3.7 8.5 - - + +
407A VAL* 4.0 2.4 - - + +
408A GLU* 1.3 77.9 - - - +
410A ASP* 1.3 78.5 + - - +
411A GLY 3.2 0.5 + - - -
412A GLU* 3.1 51.5 + - + +
413A LYS 4.5 1.7 + - - -
439A LEU 3.1 19.6 + - - +
440A SER 2.7 29.8 + - - -
441A HIS* 4.6 2.7 - - - +
442A GLY* 4.4 8.3 - - - +
569A MET* 3.7 18.5 + - + -
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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