Contacts of the strand formed by residues 51 - 60 (chain 2) 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 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452 SER* 4.0 6.3 - - - +
462 GLN 3.4 20.6 - - - +
472 VAL* 4.6 9.7 - - + +
482 VAL* 3.9 1.9 - - - +
502 GLY* 1.3 76.9 + - - -
522 ASN* 1.3 71.8 + - - +
532 TYR* 3.7 24.5 + - + +
692 VAL 3.6 0.3 - - - +
702 PHE* 3.7 1.7 - - - -
712 GLN* 2.8 62.3 + - - +
732 LEU* 5.6 2.3 - - - +
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Residues in contact with ASN 52 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442 LYS 4.0 0.3 - - - +
452 SER* 3.2 4.3 - - - -
462 GLN* 2.8 63.1 + - - +
482 VAL* 3.5 19.2 - - - +
512 THR* 1.3 74.5 - - - +
532 TYR* 1.3 60.4 - - - +
542 PHE* 3.9 13.3 - - + -
682 ARG* 3.5 31.0 + - + +
692 VAL 3.4 4.3 + - - +
702 PHE* 3.4 32.5 - - - +
832 SER* 5.0 0.8 + - - -
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Residues in contact with TYR 53 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 GLU* 4.4 11.8 + - - -
162 THR* 6.2 0.9 - - + -
192 ILE* 4.0 30.5 - - + +
432 PHE* 4.2 22.0 - + - -
442 LYS 3.6 1.6 - - - -
452 SER* 3.7 20.8 - - - -
512 THR* 3.7 21.3 - - + +
522 ASN* 1.3 73.5 - - - +
542 PHE* 1.3 60.7 + - - +
552 ILE* 4.0 19.0 + - + -
672 LEU 3.5 1.6 - - - +
682 ARG* 3.4 2.1 - - - -
692 VAL* 2.8 49.5 + - + +
712 GLN* 3.5 45.7 + - + -
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Residues in contact with PHE 54 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432 PHE* 3.0 7.4 - - - +
442 LYS* 2.9 48.7 + - + +
462 GLN* 3.9 7.9 - - + -
522 ASN* 3.9 22.0 - - + -
532 TYR* 1.3 72.6 - - - +
552 ILE* 1.3 60.9 + - - +
672 LEU 3.1 8.3 - - - +
682 ARG* 3.6 31.4 - - + -
952 LEU* 3.2 13.2 - - + +
962 THR 4.2 6.1 - - - +
972 TYR* 3.2 38.8 - + + -
982 PHE* 3.3 56.1 - + - -
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Residues in contact with ILE 55 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162 THR* 3.7 28.7 - - + +
192 ILE* 3.8 30.1 - - + -
202 ALA* 4.1 9.0 - - + +
402 ALA* 4.0 7.9 - - + -
422 SER 3.6 11.4 - - - +
432 PHE* 4.1 9.2 - - + -
532 TYR* 4.1 16.2 - - + +
542 PHE* 1.3 79.7 - - - +
562 LYS* 1.3 66.3 + - - +
572 VAL* 3.8 20.1 + - + +
652 VAL 3.6 1.2 - - - +
662 HIS* 3.3 3.5 - - - -
672 LEU* 2.8 43.0 + - + +
692 VAL* 4.4 9.6 - - + -
952 LEU* 4.0 4.9 - - - +
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Residues in contact with LYS 56 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402 ALA* 3.7 2.8 - - - -
412 VAL* 2.8 38.9 + - + +
422 SER* 3.0 30.8 + - - +
552 ILE* 1.3 71.8 - - - +
572 VAL* 1.3 60.4 + - - +
642 PHE* 4.0 18.4 - - + +
652 VAL 3.6 4.0 - - - -
662 HIS* 3.0 35.7 - - + +
902 ALA 2.8 20.5 + - - -
912 LYS* 3.5 22.9 - - - +
932 ASP* 2.8 28.4 + - - +
952 LEU* 3.9 13.2 - - + +
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Residues in contact with VAL 57 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202 ALA* 4.5 4.5 - - + -
382 PHE* 3.7 30.5 - - + -
392 LYS 3.4 28.3 - - - +
402 ALA* 4.1 3.6 - - - +
552 ILE* 3.8 17.7 - - + +
562 LYS* 1.3 80.0 - - - +
582 HIS* 1.3 66.1 + - - +
592 VAL* 3.6 3.4 + - + +
642 PHE* 3.2 9.1 - - - -
652 VAL* 2.9 35.9 + - + +
672 LEU* 3.8 31.2 - - + -
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Residues in contact with HIS 58 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372 VAL* 3.3 24.8 - - + +
382 PHE* 3.4 3.3 - - - -
392 LYS* 2.8 54.5 + - + +
412 VAL* 4.3 7.4 - - + +
562 LYS 4.3 0.2 - - - -
572 VAL* 1.3 72.0 - - - +
592 VAL* 1.3 58.8 + - - +
602 GLY* 3.4 21.6 + - - -
612 ASP 3.6 1.4 + - - -
622 GLU* 3.1 31.6 + - - -
632 ASP 3.3 11.7 + - - -
642 PHE* 3.5 30.9 - + + -
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Residues in contact with VAL 59 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352 PHE* 3.6 24.3 - - + -
362 PRO* 3.4 24.6 - - - +
372 VAL* 3.2 12.0 - - - +
382 PHE* 3.9 26.5 - - + -
572 VAL* 3.9 11.4 - - + +
582 HIS* 1.3 76.8 - - - +
602 GLY* 1.3 57.4 - - - +
632 ASP* 3.0 35.6 + - + +
642 PHE 4.2 0.7 - - - +
652 VAL* 4.0 26.7 - - + -
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Residues in contact with GLY 60 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362 PRO* 4.5 5.6 - - - -
372 VAL* 3.4 17.4 - - - +
582 HIS* 3.4 17.0 - - - -
592 VAL* 1.3 79.5 - - - +
612 ASP* 1.3 70.0 + - - +
632 ASP* 2.9 30.3 + - - +
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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