Contacts of the strand formed by residues 51 - 60 (chain 9) in PDB entry 4N6V
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 51 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459 SER* 4.0 13.0 - - - +
469 GLN 3.5 10.1 - - - +
479 VAL* 4.7 10.3 - - + +
489 VAL* 3.9 1.5 - - - +
509 GLY* 1.3 77.9 + - - -
529 ASN* 1.3 73.5 + - - +
539 TYR* 3.4 34.6 + - + +
699 VAL 3.5 1.4 - - - +
709 PHE* 3.5 1.7 - - - -
719 GLN* 2.7 48.4 + - - +
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Residues in contact with ASN 52 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449 LYS 3.9 0.7 - - - +
459 SER* 3.3 2.8 - - - -
469 GLN* 2.8 62.4 + - - +
489 VAL* 3.5 18.3 - - - +
519 THR* 1.3 72.7 - - - +
539 TYR* 1.3 61.9 + - - +
549 PHE* 3.8 20.2 + - + -
689 ARG* 3.5 29.4 + - + +
699 VAL 3.3 3.7 + - - +
709 PHE* 3.3 35.8 - - - +
839 SER* 5.0 0.6 + - - -
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Residues in contact with TYR 53 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159 GLU* 4.0 17.6 + - + -
169 THR* 6.3 1.1 - - + -
199 ILE* 3.9 32.2 - - + +
439 PHE* 4.4 17.0 - + - -
449 LYS 3.7 1.8 - - - -
459 SER* 3.6 24.2 - - - -
519 THR* 3.4 23.8 + - + +
529 ASN* 1.3 74.4 - - - +
549 PHE* 1.3 62.8 + - - +
559 ILE* 4.0 19.9 + - + +
679 LEU 3.4 3.3 - - - +
689 ARG* 3.4 1.1 - - - -
699 VAL* 2.7 45.4 + - + +
719 GLN* 3.0 41.6 + - + -
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Residues in contact with PHE 54 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439 PHE* 3.1 6.6 - - - +
449 LYS* 2.8 49.4 + - + +
469 GLN* 3.7 21.5 - - - -
529 ASN* 3.8 14.8 - - + -
539 TYR* 1.3 76.9 - - - +
559 ILE* 1.3 58.4 + - - +
679 LEU 3.1 4.9 - - - +
689 ARG* 3.6 28.3 - - + -
959 LEU* 3.4 12.4 - - + +
969 THR 4.3 1.1 - - - +
979 TYR* 3.3 41.7 - + + -
989 PHE* 3.3 57.0 - + - -
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Residues in contact with ILE 55 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169 THR* 3.7 30.5 - - + +
199 ILE* 3.7 35.9 - - + -
209 ALA* 4.2 7.4 - - + +
409 ALA* 3.8 7.2 - - + -
429 SER 3.5 11.2 - - - +
439 PHE* 4.2 2.2 - - + -
539 TYR* 4.1 17.3 - - + +
549 PHE* 1.3 79.1 - - - +
569 LYS* 1.3 64.6 + - - +
579 VAL* 3.6 21.4 + - + -
659 VAL 3.5 1.9 - - - +
669 HIS* 3.2 3.6 - - - -
679 LEU* 2.8 44.3 + - + +
699 VAL* 4.5 7.9 - - + -
959 LEU* 3.9 4.8 - - - +
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Residues in contact with LYS 56 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409 ALA* 3.6 2.8 - - - -
419 VAL* 2.8 47.6 + - + +
429 SER* 2.9 27.0 + - - +
559 ILE* 1.3 70.9 - - - +
579 VAL* 1.3 56.4 + - - +
649 PHE* 4.0 20.7 - - + +
659 VAL 3.6 3.4 - - - +
669 HIS* 3.0 32.2 - - + +
909 ALA 2.7 29.0 + - - -
919 LYS* 3.5 16.2 - - - +
939 ASP* 2.8 25.4 + - - +
959 LEU* 3.9 12.4 - - + +
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Residues in contact with VAL 57 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209 ALA* 4.3 5.4 - - + -
389 PHE* 3.7 32.3 - - + -
399 LYS 3.5 17.3 - - - +
409 ALA* 4.2 4.9 - - - +
559 ILE* 3.6 20.6 - - + +
569 LYS* 1.3 77.8 - - - +
589 HIS* 1.3 75.1 + - - +
599 VAL* 3.6 2.7 + - + +
649 PHE* 3.1 9.7 - - - -
659 VAL* 2.8 41.1 + - + +
679 LEU* 3.8 27.6 - - + -
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Residues in contact with HIS 58 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379 VAL* 3.7 15.7 - - + +
389 PHE* 3.3 8.3 + - - -
399 LYS* 2.8 57.0 + - + +
419 VAL* 4.4 6.9 - - + +
569 LYS 4.3 0.4 + - - -
579 VAL* 1.3 70.7 - - - +
599 VAL* 1.3 58.7 + - - +
609 GLY* 3.4 21.0 + - - -
619 ASP 3.5 1.8 + - - -
629 GLU* 3.4 29.8 - - - -
639 ASP 3.4 10.5 + - - -
649 PHE* 3.5 32.4 - + + -
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Residues in contact with VAL 59 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359 PHE* 3.6 26.1 - - + -
369 PRO* 3.0 25.1 - - - +
379 VAL* 3.3 11.2 - - - +
389 PHE* 3.7 31.0 - - + -
579 VAL* 3.9 9.9 - - + +
589 HIS* 1.3 79.8 - - - +
609 GLY* 1.3 57.0 + - - +
639 ASP* 2.9 36.1 + - + +
649 PHE 4.2 1.8 - - - +
659 VAL* 4.2 20.2 - - + -
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Residues in contact with GLY 60 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369 PRO* 4.7 4.9 - - - -
379 VAL* 3.2 19.2 - - - +
589 HIS* 3.4 11.4 - - - -
599 VAL* 1.3 79.8 - - - +
619 ASP* 1.3 80.5 + - - +
639 ASP* 2.9 21.3 + - - +
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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