Contacts of the strand formed by residues 424 - 432 (chain D) in PDB entry 3VBB
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 HIS 424 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D VAL 3.9 0.3 - - - +
329D TYR* 3.6 2.9 - - - -
330D SER* 2.9 37.1 + - - +
332D PRO* 3.4 45.7 - - + +
337D SER* 3.2 39.3 + - - -
338D TRP* 5.8 2.2 - + - -
397D ASN* 4.7 1.1 - - - +
399D THR* 3.3 28.0 - - + -
400D ASP* 3.5 28.7 + - + -
423D VAL* 1.3 78.4 - - - +
425D MET* 1.3 61.1 + - - +
426D LEU* 4.3 1.6 + - + +
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Residues in contact with MET 425 (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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273D GLU* 5.5 1.6 - - - +
277D ALA* 5.0 8.3 - - + -
328D VAL 3.4 6.1 - - - +
329D TYR* 3.4 34.5 - - + +
397D ASN* 4.5 0.2 - - - -
398D CYS* 3.2 29.8 + - - +
399D THR 3.1 8.4 + - - +
402D GLN* 3.2 41.8 + - + +
403D ALA* 3.9 20.0 - - + +
406D LEU* 4.5 12.6 - - + -
408D ILE* 3.8 17.3 - - - -
423D VAL* 4.2 4.5 - - + -
424D HIS* 1.3 78.4 - - - +
426D LEU* 1.3 65.8 + - - +
427D ASN* 5.6 0.2 + - - -
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Residues in contact with LEU 426 (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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327D PHE* 3.6 2.3 - - - +
328D VAL* 2.9 51.0 + - + +
330D SER* 4.3 16.6 - - - +
337D SER* 3.3 19.5 - - - +
340D MET* 4.1 13.9 - - + -
341D PHE* 3.7 18.4 - - + -
344D MET* 3.6 17.0 - - - -
396D SER 3.5 7.6 - - - +
397D ASN* 3.3 37.2 - - + +
424D HIS 4.4 3.1 - - - +
425D MET* 1.3 79.9 - - - +
427D ASN* 1.3 64.7 + - - +
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Residues in contact with ASN 427 (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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273D GLU* 3.8 28.9 + - + +
325D GLU* 4.2 8.7 - - - +
326D GLN 3.4 4.0 - - - -
327D PHE* 3.6 22.7 - - + -
344D MET* 3.9 4.0 - - - -
394D SER 3.9 1.0 - - - +
395D CYS* 3.6 0.7 - - - -
396D SER* 2.8 48.4 + - - -
398D CYS* 4.3 12.3 - - - -
402D GLN* 5.3 1.2 - - - +
426D LEU* 1.3 77.8 - - - +
428D ALA* 1.3 62.3 + - - +
429D THR* 5.0 2.9 + - - +
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Residues in contact with ALA 428 (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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325D GLU* 3.4 7.0 - - - +
326D GLN* 2.8 48.1 + - - +
344D MET* 3.6 20.7 - - + +
393D VAL* 4.9 4.5 - - + -
394D SER 3.0 11.9 - - - +
395D CYS* 3.7 13.5 - - + -
427D ASN* 1.3 76.1 - - - +
429D THR* 1.3 66.4 + - - +
430D MET 3.7 0.2 - - - -
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Residues in contact with THR 429 (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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271D THR* 4.8 3.8 - - + -
323D LYS* 3.9 27.2 - - + +
324D ILE 3.9 3.8 - - - -
325D GLU* 3.4 28.7 - - + +
391D GLU* 4.9 2.8 + - - -
392D LEU 3.7 4.2 + - - +
393D VAL* 3.0 29.3 - - - +
394D SER* 3.0 27.5 + - - +
427D ASN* 5.1 3.4 - - - +
428D ALA* 1.3 72.7 - - - +
430D MET* 1.3 61.7 + - - +
431D CYS 5.1 1.8 - - - -
432D ALA* 6.3 0.2 - - - -
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Residues in contact with MET 430 (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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211D ALA* 4.3 7.4 - - + -
214D THR* 3.9 18.2 - - + -
215D LEU* 3.5 33.2 - - + -
324D ILE* 3.1 14.6 + - + +
326D GLN* 3.7 25.6 - - + +
347D THR* 4.5 6.7 - - - +
348D ALA* 4.6 10.3 - - + -
351D PHE* 3.1 50.9 - - + -
352D TYR* 2.7 25.8 + - - -
392D LEU 4.5 0.2 - - - -
393D VAL* 3.5 11.0 - - - +
428D ALA 3.7 3.6 + - - -
429D THR* 1.3 73.0 - - - +
431D CYS* 1.3 65.7 + - + +
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Residues in contact with CYS 431 (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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207D LEU* 4.3 17.3 - - - -
211D ALA* 4.8 2.5 - - + -
323D LYS* 3.2 6.7 - - - -
324D ILE* 2.8 50.4 + - + +
351D PHE* 4.5 10.3 - - + -
352D TYR* 3.7 6.5 - - - +
392D LEU 4.9 0.2 - - - -
429D THR 3.7 1.1 - - - -
430D MET* 1.3 84.8 - - + +
432D ALA* 1.3 65.1 + - - +
433D THR* 3.6 12.7 + - - +
436D THR* 3.3 31.9 - - - -
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Residues in contact with ALA 432 (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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321D PHE* 4.6 16.2 - - + -
322D GLU 3.8 6.7 - - - +
323D LYS* 4.4 11.4 - - + +
392D LEU* 4.6 10.3 + - - +
429D THR* 5.7 2.4 + - - +
430D MET 4.4 0.2 - - - -
431D CYS* 1.3 70.4 - - - +
433D THR* 1.3 67.9 + - - +
434D THR* 3.2 1.6 - - - +
435D ARG* 3.0 39.5 + - + +
436D THR* 3.1 15.1 + - - -
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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