Contacts of the strand formed by residues 407 - 411 (chain A) in PDB entry 4ZZH
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 MET 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A PHE* 3.5 4.5 - - - -
369A ALA* 3.3 24.2 - - + +
371A CYS* 3.5 29.4 - - - +
376A TYR* 3.2 23.8 - - - +
378A VAL* 3.6 22.4 - - + -
383A VAL* 4.2 12.5 - - + +
393A PRO* 3.0 40.4 + - + +
394A ARG 3.6 24.9 - - - +
395A CYS* 4.1 13.7 - - - -
396A PRO* 4.8 4.5 - - + -
406A ILE* 1.3 70.4 - - - +
408A LYS* 1.3 59.7 - - - +
409A PRO* 3.5 9.0 - - - +
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Residues in contact with LYS 408 (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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299A ILE* 4.0 2.9 - - + -
302A PHE* 4.0 16.4 - - + -
309A PHE* 5.5 0.4 - - + -
369A ALA* 3.8 1.3 - - - -
370A SER 2.8 37.8 + - - +
372A LEU* 3.6 33.2 - - + -
406A ILE 3.5 1.4 + - - -
407A MET* 1.3 72.7 - - - +
409A PRO* 1.3 79.2 + - + +
410A GLU* 3.4 8.2 + - - +
411A ILE 2.8 29.5 + - - +
413A PHE* 3.5 30.1 - - + -
416A GLU* 3.6 22.2 + - - -
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Residues in contact with PRO 409 (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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309A PHE* 4.1 17.6 - - + -
310A PHE* 4.1 17.7 - - + -
317A TYR* 5.3 2.0 - - + +
365A SER 4.3 4.7 - - - +
366A PHE* 4.0 32.5 - - + +
368A THR 3.4 11.2 - - - +
369A ALA* 3.8 8.0 - - + -
383A VAL* 5.4 3.1 - - + -
387A ILE* 4.7 8.5 - - + -
407A MET 3.5 9.0 - - - +
408A LYS* 1.3 100.6 + - + +
410A GLU* 1.3 53.1 + - - +
411A ILE* 2.6 25.9 + - + +
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Residues in contact with GLU 410 (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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364A GLY* 3.2 18.2 - - - -
365A SER 3.3 11.8 + - - +
368A THR* 2.9 40.6 + - - +
370A SER* 3.5 31.6 - - - +
377A LYS* 3.3 34.1 + - - -
408A LYS* 4.1 6.3 - - - +
409A PRO* 1.3 67.4 - - - +
411A ILE* 1.3 62.9 + - - +
412A VAL* 3.6 2.1 + - - +
419A PRO* 5.9 0.9 - - - +
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Residues in contact with ILE 411 (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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297A PHE* 4.3 12.6 - - + -
309A PHE* 4.4 15.0 - - + -
347A ILE* 3.9 20.4 - - + -
363A HIS 3.9 6.1 - - - +
365A SER* 3.5 32.3 - - - +
366A PHE* 3.9 24.9 - - + -
408A LYS* 2.8 27.2 + - - -
409A PRO* 2.6 16.8 + - + +
410A GLU* 1.3 72.9 - - - +
412A VAL* 1.3 74.8 + - - +
413A PHE* 3.0 28.6 + - + -
416A GLU* 3.3 1.4 - - - +
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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