Contacts of the strand formed by residues 414 - 418 (chain S) in PDB entry 5L4K
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 TYR 414 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331R ASP* 3.2 12.5 + - - -
335R SER* 4.5 8.0 - - - -
346R LYS* 3.4 5.1 + - - -
347R ILE* 2.9 44.9 - - + +
348R ASP* 4.3 0.2 - - - -
349R LYS* 4.2 16.8 - - + +
409S MET* 6.4 0.2 - - - -
410S ILE* 3.0 33.2 + - + +
411S SER 3.0 18.3 - - - +
413S SER* 1.3 94.3 - - - +
415S SER* 1.3 62.8 + - - +
416S ARG 4.3 10.1 - - - +
417S ILE* 3.6 24.9 - - + -
425S LYS* 2.7 45.4 + - + +
460S SER* 3.7 1.5 + - - +
462S GLU* 3.1 11.4 - - - +
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Residues in contact with SER 415 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346R LYS* 3.0 33.4 + - - +
347R ILE 2.8 13.2 + - - -
348R ASP* 4.4 7.4 - - - -
355R GLU* 4.3 15.7 + - - -
414S TYR* 1.3 71.0 - - - +
416S ARG* 1.3 63.5 + - - +
460S SER* 2.7 44.6 + - - +
462S GLU* 4.5 0.4 - - - -
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Residues in contact with ARG 416 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347R ILE 4.3 0.7 - - - +
348R ASP* 3.2 36.2 + - + +
349R LYS 3.4 2.6 + - - -
350R VAL* 4.5 20.3 - - + +
351R ASN* 3.8 22.4 - - - +
414S TYR* 4.4 2.9 - - - +
415S SER* 1.3 92.3 - - - +
417S ILE* 1.3 64.8 + - - +
457S TYR* 3.2 42.9 + - + -
458S VAL* 3.1 12.1 - - - +
459S GLN* 3.0 36.3 + - + -
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Residues in contact with ILE 417 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349R LYS* 3.9 17.7 - - + +
350R VAL* 4.5 6.1 - - - -
410S ILE* 4.4 12.6 - - + -
414S TYR* 3.6 39.0 - - + -
416S ARG* 1.3 76.7 - - - +
418S SER* 1.3 70.1 + - - +
421S ASP* 3.7 27.6 - - + +
422S ILE* 3.5 32.3 - - + +
425S LYS* 4.1 10.1 - - - -
457S TYR* 3.2 6.8 - - - -
458S VAL* 2.9 36.7 + - + +
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Residues in contact with SER 418 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349R LYS 5.0 2.8 + - - -
350R VAL* 4.1 17.8 - - - +
417S ILE* 1.3 80.7 - - - +
419S LEU* 1.3 66.6 + - - +
420S ALA* 4.2 9.2 - - - -
421S ASP* 3.1 27.6 + - - +
422S ILE* 3.2 12.8 + - - +
456S GLY 3.5 12.1 + - - -
457S TYR* 4.2 2.2 - - - +
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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