Contacts of the strand formed by residues 434 - 440 (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 VAL 434 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D ILE* 4.2 13.7 - - + -
96D PRO 3.3 25.1 - - - +
97D GLN 3.7 5.8 - - - -
99D LEU* 3.9 28.0 - - + -
111D PHE* 4.9 0.2 - - + -
113D LEU* 3.9 33.2 - - + -
424D LYS* 3.1 6.7 - - - -
425D ILE* 2.7 50.4 + - + +
433D GLU* 1.3 76.8 - - - +
435D GLU* 1.3 61.6 + - - +
436D VAL* 3.5 8.4 + - + +
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Residues in contact with GLU 435 (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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71D LYS* 5.3 4.7 + - - -
97D GLN 3.0 10.5 + - - +
98D GLN* 3.3 30.5 + - + +
99D LEU* 3.0 28.1 + - - +
422D SER* 4.2 12.6 + - - -
423D PHE 3.8 3.1 - - - +
424D LYS* 3.8 30.9 + - + +
433D GLU* 4.0 1.6 - - + +
434D VAL* 1.3 70.8 - - - +
436D VAL* 1.3 59.3 + - - +
437D ILE* 3.6 27.3 - - - +
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Residues in contact with VAL 436 (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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99D LEU* 3.6 15.5 - - + +
101D LEU* 4.0 31.0 - - + -
111D PHE* 3.8 23.8 - - + -
410D ILE* 4.4 1.1 - - + -
422D SER* 3.3 2.6 - - - -
423D PHE* 2.8 64.5 + - + +
425D ILE* 3.9 17.7 - - + -
434D VAL* 4.1 7.2 - - + +
435D GLU* 1.3 74.1 - - - +
437D ILE* 1.3 63.6 + - - +
438D LEU* 4.2 6.5 - - + -
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Residues in contact with ILE 437 (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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98D GLN* 4.0 19.3 - - + +
99D LEU 2.9 14.3 + - - +
100D VAL* 4.1 25.5 - - + +
101D LEU* 2.8 32.7 + - - +
420D SER* 5.0 6.1 - - - -
421D ASP 3.3 4.9 - - - +
422D SER* 3.9 14.1 - - - +
435D GLU* 3.6 25.8 - - - +
436D VAL* 1.3 73.2 - - - +
438D LEU* 1.3 67.4 - - - +
439D GLN* 4.5 9.4 - - + +
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Residues in contact with LEU 438 (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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101D LEU* 3.4 24.5 - - + +
103D LEU* 4.1 16.6 - - + -
369D LEU* 5.0 3.8 - - + -
373D VAL* 4.6 15.0 - - + -
410D ILE* 4.2 9.6 - - + -
419D ASP 4.5 0.2 - - - +
420D SER* 3.2 12.5 - - - -
421D ASP* 2.6 41.9 + - + +
423D PHE* 3.6 28.0 - - + -
436D VAL* 4.2 10.3 - - + -
437D ILE* 1.3 75.8 - - - +
439D GLN* 1.3 63.8 + - - +
440D TYR* 3.7 34.9 - - + +
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Residues in contact with GLN 439 (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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100D VAL* 3.6 22.7 - - + +
101D LEU 2.8 9.1 + - - +
102D ARG* 3.1 47.2 + - + +
103D LEU* 3.0 24.2 + - - +
419D ASP 5.0 0.9 - - - -
420D SER* 4.4 14.6 - - - +
437D ILE* 4.5 7.0 - - + +
438D LEU* 1.3 80.2 - - - +
440D TYR* 1.3 64.7 + - - +
441D ILE* 3.8 0.7 + - - +
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Residues in contact with TYR 440 (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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102D ARG* 5.3 2.8 + - - -
103D LEU* 3.4 17.3 - - + +
104D ARG 5.8 1.1 - - - +
370D SER* 3.4 8.3 + - - -
373D VAL* 4.0 20.3 - - + +
412D SER* 4.2 14.6 - - - +
414D LYS 5.4 0.9 - - - +
415D CYS* 4.7 2.7 - - - -
416D PRO* 4.1 29.2 - - + -
417D LYS* 3.5 18.4 - - + +
418D LYS* 6.0 1.0 - - - -
419D ASP 3.4 26.1 + - - +
421D ASP* 2.7 41.8 + - + +
438D LEU* 3.7 24.8 - - + +
439D GLN* 1.3 74.3 - - - +
441D ILE* 1.3 61.3 + - - +
442D CYS* 3.6 17.2 + - - -
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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