Contacts of the strand formed by residues 441 - 447 (chain B) in PDB entry 3N9V
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 441 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B THR* 4.5 12.8 - - + -
393B SER 3.0 5.1 + - - -
394B ILE* 3.3 25.8 - - + -
395B CYS 2.9 25.5 + - - -
439B HIS* 3.6 5.2 - - - +
440B ASP* 1.3 82.2 - - + +
442B ILE* 1.3 64.6 + - - +
443B LEU* 4.1 14.1 - - + -
529B LYS 3.8 2.7 - - - -
531B LYS 4.5 7.9 - - - +
533B ILE* 4.2 16.4 - - + -
558B ILE* 3.8 45.1 - - + -
559B GLY 5.2 1.3 - - - +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B CYS* 3.2 9.9 - - + +
397B VAL* 4.8 4.0 - - + -
436B ILE* 3.7 44.9 - - + +
437B SER* 4.0 20.0 - - - +
439B HIS* 4.2 8.3 - - + +
441B VAL* 1.3 77.8 - - - +
443B LEU* 1.3 73.4 + - - +
444B TRP* 4.5 1.6 - - + +
491B PHE* 3.9 22.7 - - + -
528B TRP* 3.2 9.2 - - - +
529B LYS* 3.0 59.3 + - + +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B PHE* 4.4 21.3 - - + -
269B ALA* 4.6 19.5 - - + -
298B CYS* 4.4 22.7 - - + -
394B ILE* 5.2 0.4 - - + -
395B CYS 3.1 6.8 + - - +
396B VAL* 3.4 19.4 - - + +
397B VAL 2.9 25.0 + - - +
441B VAL* 4.1 17.7 - - + +
442B ILE* 1.3 84.2 - - - +
444B TRP* 1.3 61.8 + - - +
445B LEU* 5.5 2.0 - - + -
526B ILE* 5.5 2.9 - - + -
527B LEU 3.8 3.4 - - - +
528B TRP* 3.8 17.3 - - + -
533B ILE* 5.0 1.3 - - + -
556B PHE* 4.6 15.9 - - + -
558B ILE* 4.3 11.4 - - + -
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Residues in contact with TRP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B VAL* 3.5 29.8 - - + +
399B SER* 2.8 32.5 + - - -
401B LEU* 5.6 0.7 - - + -
415B TYR* 3.7 38.1 - + + -
418B ILE* 3.7 28.9 - - + -
419B CYS* 3.9 11.2 - - - -
436B ILE* 3.6 25.4 - - + -
442B ILE* 4.1 1.3 - - + -
443B LEU* 1.3 72.7 - - - +
445B LEU* 1.3 74.4 + - - +
448B LEU* 4.0 8.9 - - + +
488B PHE* 3.8 23.0 - + + -
491B PHE* 4.2 27.1 - + + -
525B ARG 4.0 0.2 - - - +
526B ILE* 3.3 3.3 - - - +
527B LEU* 2.8 40.9 + - - +
528B TRP* 4.8 0.2 - - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ALA* 4.3 14.1 - - + -
270B GLY 3.1 27.4 - - - +
271B THR* 3.7 10.8 - - - -
298B CYS* 4.3 12.8 - - + +
300B GLY* 3.7 12.3 - - - -
349B LEU* 4.3 4.5 - - + -
396B VAL* 4.2 22.4 - - + -
397B VAL 2.9 14.9 + - - +
398B ASN* 3.4 21.9 - - + +
399B SER* 3.2 20.3 + - - -
443B LEU* 5.5 3.4 - - + -
444B TRP* 1.3 86.8 + - - +
446B GLY* 1.3 58.2 + - - +
448B LEU* 4.6 1.6 - - - -
525B ARG 3.3 9.9 - - - +
526B ILE* 4.1 15.5 - - + -
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Residues in contact with GLY 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B THR* 3.3 20.5 + - - -
302B GLN* 3.3 9.9 - - - -
398B ASN* 3.6 1.6 - - - -
399B SER 3.4 6.5 - - - -
445B LEU* 1.3 78.8 - - - +
447B ASP* 1.3 61.8 + - - -
448B LEU* 3.4 6.8 + - - +
524B ASP* 3.4 3.3 - - - -
525B ARG 3.0 31.8 + - - +
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Residues in contact with ASP 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B ASN* 2.5 29.8 + - - -
302B GLN* 3.4 21.4 - - + +
399B SER 3.1 8.7 + - - -
400B HIS* 3.5 21.5 + - + -
401B LEU 3.1 21.8 + - - -
446B GLY* 1.3 68.0 - - - -
448B LEU* 1.3 57.2 + - - +
449B ASN* 3.3 25.2 + - - +
523B CYS* 3.4 11.2 - - - +
524B ASP* 3.6 14.1 - - - +
549B HIS* 3.3 11.0 + - - -
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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