Contacts of the strand formed by residues 51 - 60 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455 SER* 4.0 11.0 - - - +
465 GLN 3.4 11.9 - - - +
475 VAL* 4.7 11.1 - - + +
485 VAL* 4.4 0.4 - - - -
505 GLY* 1.3 77.7 + - - -
525 ASN* 1.3 77.3 + - - +
535 TYR* 3.5 29.1 + - + +
695 VAL 3.6 0.5 - - - +
705 PHE* 3.7 1.7 - - - -
715 GLN* 2.9 50.6 + - - +
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Residues in contact with ASN 52 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455 SER* 3.1 5.2 - - - -
465 GLN* 2.6 69.5 + - + +
485 VAL* 3.8 17.5 - - - +
515 THR* 1.3 72.4 + - - +
535 TYR* 1.3 61.6 + - - +
545 PHE* 3.9 12.1 + - + -
685 ARG* 3.5 29.6 + - + +
695 VAL 3.5 2.8 + - - +
705 PHE* 3.4 34.2 - - - +
835 SER* 5.2 1.2 + - - -
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Residues in contact with TYR 53 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155 GLU* 3.7 16.4 + - - -
165 THR* 6.4 0.7 - - + -
195 ILE* 3.9 30.7 - - + -
435 PHE* 4.5 16.4 - + - -
445 LYS 3.9 2.0 - - - -
455 SER* 3.6 25.1 - - - -
515 THR* 3.5 21.6 + - + +
525 ASN* 1.3 72.3 - - - +
545 PHE* 1.3 63.4 + - - +
555 ILE* 3.6 16.2 - - + +
675 LEU 3.6 2.3 - - - +
695 VAL* 2.8 48.1 + - + +
715 GLN* 3.2 47.1 + - + -
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Residues in contact with PHE 54 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435 PHE* 3.0 8.7 - - - +
445 LYS* 2.9 46.5 + - + +
465 GLN* 4.0 7.6 - - + -
525 ASN* 3.9 22.0 - - + -
535 TYR* 1.3 73.1 - - - +
555 ILE* 1.3 59.5 + - - +
675 LEU 3.2 5.2 - - - +
685 ARG* 3.4 31.4 - - + -
955 LEU* 3.5 18.8 - - + +
965 THR 4.4 4.0 - - - +
975 TYR* 3.4 40.6 - + - -
985 PHE* 3.2 56.3 - + - -
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Residues in contact with ILE 55 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165 THR* 3.8 30.5 - - + +
195 ILE* 3.6 31.4 - - + -
205 ALA* 4.1 9.2 - - + +
405 ALA* 4.1 10.1 - - + -
425 SER 3.4 10.3 - - - +
435 PHE* 4.3 4.7 - - + -
535 TYR* 3.6 19.7 - - + +
545 PHE* 1.3 79.5 - - - +
565 LYS* 1.3 62.1 + - - +
575 VAL* 3.6 23.2 + - + +
655 VAL 3.5 0.9 - - - +
665 HIS* 3.2 4.0 - - - -
675 LEU* 2.8 41.2 + - + +
695 VAL* 4.6 4.7 - - + -
955 LEU* 4.1 5.6 - - - +
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Residues in contact with LYS 56 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405 ALA* 3.7 2.1 - - - -
415 VAL* 2.9 43.2 + - + +
425 SER* 2.8 29.6 + - - +
555 ILE* 1.3 69.7 - - - +
575 VAL* 1.3 60.3 + - - +
645 PHE* 3.9 18.6 - - + +
655 VAL 3.7 2.0 - - - -
665 HIS* 2.7 43.9 + - + +
895 LYS* 4.4 0.2 - - - +
905 ALA 2.9 28.7 + - - -
915 LYS* 3.6 15.0 - - - +
935 ASP* 2.9 23.0 + - - +
955 LEU* 3.9 12.3 - - + +
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Residues in contact with VAL 57 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205 ALA* 4.2 6.5 - - + -
385 PHE* 3.8 30.7 - - + -
395 LYS 3.4 18.8 - - - +
405 ALA* 4.3 2.5 - - - +
555 ILE* 3.7 16.2 - - + +
565 LYS* 1.3 78.1 - - - +
585 HIS* 1.3 71.9 + - - +
595 VAL* 3.6 2.7 + - + +
645 PHE* 3.1 7.7 - - - -
655 VAL* 2.7 45.1 + - + +
675 LEU* 3.5 34.8 - - + -
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Residues in contact with HIS 58 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375 VAL* 3.4 26.1 - - + +
385 PHE* 3.3 7.4 + - - -
395 LYS* 2.8 46.0 + - + +
415 VAL* 4.4 6.5 - - + +
565 LYS 4.2 0.2 + - - -
575 VAL* 1.3 71.5 - - - +
595 VAL* 1.3 58.9 + - - +
605 GLY* 3.5 19.9 + - - -
615 ASP 3.9 1.8 + - - -
625 GLU* 3.1 36.6 - - + -
635 ASP 3.1 15.2 + - - -
645 PHE* 3.6 28.5 - + + -
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Residues in contact with VAL 59 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355 PHE* 3.5 32.8 - - + -
365 PRO* 3.9 16.5 - - - +
375 VAL* 3.2 14.2 - - - +
385 PHE* 3.6 31.6 - - + -
575 VAL* 4.1 8.3 - - + +
585 HIS* 1.3 78.4 - - - +
605 GLY* 1.3 58.9 + - - +
635 ASP* 3.0 30.0 + - + +
645 PHE* 4.2 9.4 - - - +
655 VAL* 4.4 11.9 - - + -
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Residues in contact with GLY 60 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365 PRO* 5.0 4.7 - - - -
375 VAL* 4.0 13.9 - - - +
585 HIS* 3.5 15.8 + - - -
595 VAL* 1.3 80.2 - - - +
615 ASP* 1.3 72.0 + - - +
625 GLU 3.3 2.7 - - - -
635 ASP* 3.0 21.0 + - - +
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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