Contacts of the strand formed by residues 420 - 427 (chain D) in PDB entry 3VI4
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 SER 420 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419D ASP* 1.3 82.8 - - - +
421D ASP* 1.3 69.8 + - - +
422D SER* 5.5 1.4 + - - -
437D ILE* 5.0 6.5 - - - +
438D LEU 3.2 14.6 - - - -
439D GLN* 4.4 15.9 - - - +
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Residues in contact with ASP 421 (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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370D SER* 2.7 23.7 + - - -
416D PRO* 5.2 0.7 - - - +
419D ASP* 6.3 0.4 - - - -
420D SER* 1.3 77.4 - - - +
422D SER* 1.3 66.5 + - - +
423D PHE* 5.8 0.7 - - + -
436D VAL 3.8 0.4 - - - +
437D ILE* 3.3 4.7 - - - +
438D LEU* 2.6 48.4 + - + +
440D TYR* 2.7 35.7 + - - +
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Residues in contact with SER 422 (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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368D LYS 4.8 3.3 - - - +
420D SER* 5.5 1.6 + - - -
421D ASP* 1.3 82.5 + - - +
423D PHE* 1.3 65.8 + - - +
424D LYS* 6.0 3.4 - - - -
435D GLU* 4.2 17.8 + - - -
436D VAL 3.3 8.3 - - - -
437D ILE* 3.9 12.6 - - - +
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Residues in contact with PHE 423 (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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366D ASN* 3.8 19.3 - - + -
367D GLY* 4.0 11.0 - - - -
368D LYS 3.9 16.2 - - - +
369D LEU* 3.4 27.4 - - + -
375D ILE* 4.1 5.4 - - + -
410D ILE* 3.3 28.3 - - + -
421D ASP* 5.8 0.7 - - + -
422D SER* 1.3 76.9 - - - +
424D LYS* 1.3 69.3 + - - +
425D ILE* 3.9 25.1 - - + -
435D GLU* 3.8 0.3 - - - -
436D VAL* 2.8 54.5 + - + +
438D LEU* 3.6 28.7 - - + -
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Residues in contact with LYS 424 (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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365D GLU* 3.5 2.4 - - - +
366D ASN* 3.5 3.5 - - - -
367D GLY* 3.3 22.1 + - - +
422D SER* 5.8 3.1 - - - -
423D PHE* 1.3 83.5 - - - +
425D ILE* 1.3 63.7 + - - +
426D ARG* 3.7 3.3 + - + +
433D GLU* 3.2 38.9 + - + +
434D VAL 3.1 10.3 - - - +
435D GLU* 3.8 30.6 + - + +
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Residues in contact with ILE 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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111D PHE* 3.8 18.8 - - + -
113D LEU* 4.1 10.8 - - + -
364D LEU* 4.0 28.9 - - + -
365D GLU 3.3 7.2 - - - +
366D ASN* 3.9 2.7 - - + -
375D ILE* 4.4 0.2 - - + -
377D TYR* 3.8 21.1 - - - +
408D ILE* 3.7 28.3 - - + -
423D PHE* 3.9 27.3 + - + -
424D LYS* 1.3 71.6 - - - +
426D ARG* 1.3 61.7 + - - +
427D PRO* 4.6 1.2 - - + +
432D GLU 4.4 0.2 - - - +
433D GLU* 3.6 1.7 - - - -
434D VAL* 2.7 49.6 + - + +
436D VAL* 3.9 7.4 - - + -
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Residues in contact with ARG 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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307D SER* 2.8 31.1 + - - +
308D GLU 5.6 1.3 - - - -
310D ASN* 2.8 30.3 + - - -
364D LEU* 4.4 3.6 - - - -
365D GLU* 2.8 58.1 + - + +
424D LYS* 4.5 3.6 - - + +
425D ILE* 1.3 77.2 - - - +
427D PRO* 1.3 69.5 - - - +
428D LEU* 3.3 19.7 + - - +
429D GLY 3.8 9.1 - - - +
430D PHE 2.9 29.8 + - - +
431D THR* 4.5 2.6 - - - +
432D GLU 3.9 7.6 - - - +
433D GLU* 3.9 29.2 - - + -
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Residues in contact with PRO 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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94D ILE* 4.0 26.5 - - + -
113D LEU* 6.5 0.2 - - + -
115D PHE* 4.1 8.7 - - + -
362D VAL* 4.2 12.3 - - + -
363D ILE 3.2 9.4 - - - +
364D LEU* 3.7 18.6 - - + -
425D ILE 4.6 1.6 - - - +
426D ARG* 1.3 82.4 - - - +
428D LEU* 1.3 67.7 + - - +
429D GLY 3.1 2.6 + - - -
430D PHE* 3.1 45.7 + - + +
432D GLU* 3.5 16.8 - - + +
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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