Contacts of the strand formed by residues 440 - 445 (chain A) in PDB entry 5G04
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 LYS 440 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ILE* 4.1 24.5 - - + -
433A THR 3.8 2.0 - - - +
434A SER* 4.7 10.5 - - - +
438A GLY* 4.7 5.6 - - - -
439A GLN* 1.3 99.9 - - - +
441A PHE* 1.3 69.0 + - - +
442A LEU 3.9 0.4 - - - -
456A LYS* 3.5 1.9 - - - -
457A PHE* 3.0 46.7 + - + +
458A GLN* 3.8 36.2 - - - +
459A GLU* 4.6 10.4 - - + +
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Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A PHE 3.3 0.2 - - - +
433A THR* 2.8 43.0 + - - +
435A ASP* 3.3 37.2 - - - -
439A GLN* 3.6 21.1 - - + -
440A LYS* 1.3 75.0 - - - +
442A LEU* 1.3 62.6 + - - +
443A CYS* 3.1 24.5 - - - -
454A CYS* 4.4 14.6 - - + -
455A VAL 3.3 20.0 - - - +
456A LYS* 3.5 23.3 - - + -
472A THR* 5.5 0.2 - - - -
502A GLY* 3.9 20.9 - - - +
503A VAL* 3.7 29.4 - - + -
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PHE* 4.0 8.1 - - + -
255A ILE* 3.7 43.7 - - + -
257A MET* 4.6 7.0 - - - -
268A VAL* 5.4 0.4 - - + -
430A VAL* 3.6 27.4 - - + +
431A PHE 3.6 7.0 - - - +
432A ILE* 3.9 16.1 - - + +
440A LYS 3.9 1.0 - - - -
441A PHE* 1.3 71.3 - - - +
443A CYS* 1.3 75.4 + - - +
444A PHE* 3.8 13.4 - - + -
455A VAL* 2.9 33.5 + - - +
457A PHE* 3.6 31.7 - - + -
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Residues in contact with CYS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A VAL* 3.0 31.4 - - - +
431A PHE* 3.4 41.9 + - + -
433A THR* 4.7 0.9 - - - -
441A PHE* 3.1 23.8 - - - -
442A LEU* 1.3 75.2 - - - +
444A PHE* 1.3 67.5 + - - +
445A LEU* 4.2 0.9 - - + -
452A LEU* 5.4 3.6 - - + +
453A ARG 3.3 11.9 - - - +
454A CYS* 3.9 14.4 - - - -
479A ALA* 6.3 0.2 - - + -
488A MET* 3.8 16.4 - - - -
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Residues in contact with PHE 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A MET* 3.5 28.5 - - + -
266A HIS* 3.5 31.6 - + + +
268A VAL* 4.6 3.1 - - + -
414A THR* 4.0 16.6 - - - -
415A GLU 4.1 15.7 - - - -
427A ALA* 4.8 0.2 - - + -
430A VAL* 3.7 12.8 - - + -
442A LEU* 3.8 21.8 - - + -
443A CYS* 1.3 79.1 - - - +
445A LEU* 1.3 59.9 + - - +
452A LEU* 3.2 3.0 - - - -
453A ARG* 2.9 72.6 + - + +
455A VAL* 3.4 30.7 - - + -
471A VAL* 5.2 2.0 - - + -
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Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ALA* 3.3 4.4 - - - -
428A SER* 3.0 44.9 + - - +
429A LYS* 3.8 32.1 - - + +
430A VAL* 5.0 1.6 - - - +
431A PHE* 5.7 4.0 - - + -
443A CYS* 4.2 1.2 - - + -
444A PHE* 1.3 72.7 - - - +
446A VAL* 1.3 67.0 + - - +
447A GLU* 5.3 0.9 - - - +
451A GLN 3.6 18.6 - - - +
452A LEU* 3.7 22.7 - - + -
477A LYS 3.4 24.7 - - - +
478A ASP* 3.8 8.1 - - - +
479A ALA* 3.3 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