Contacts of the strand formed by residues 412 - 416 (chain A) in PDB entry 1ZVR
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 SER 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLN 4.1 2.1 + - - -
279A ALA* 3.4 6.6 - - - -
280A THR* 2.7 41.1 + - - +
306A ILE* 4.4 16.6 + - - -
307A MET* 5.5 1.3 - - - -
309A SER* 5.9 0.3 - - - -
310A ASN* 3.7 13.2 + - - +
315A LYS 4.8 4.5 + - - -
316A ILE* 3.1 17.8 - - - +
317A PHE 3.0 22.5 + - - -
411A THR* 1.3 79.5 - - - +
413A VAL* 1.3 60.5 + - - +
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Residues in contact with VAL 413 (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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280A THR 2.7 18.0 + - - +
281A ILE* 3.8 14.4 - - + -
282A THR* 3.0 24.7 + - - +
306A ILE* 6.0 0.4 - - - +
316A ILE* 4.9 0.4 - - - -
317A PHE* 3.1 9.0 - - + +
319A PHE* 3.6 22.0 - - + -
402A ILE* 3.6 27.8 - - + +
405A LYS* 3.6 32.5 - - + -
406A VAL* 3.9 5.6 - - + -
411A THR 3.8 4.7 - - - +
412A SER* 1.3 79.7 - - - +
414A VAL* 1.3 62.2 + - - +
415A VAL* 4.5 3.4 - - + -
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PRO* 4.7 5.8 - - + -
282A THR* 3.3 21.8 - - - +
284A CYS* 3.7 28.9 - - - -
303A LEU* 4.3 13.0 - - + -
306A ILE* 4.2 10.3 - - + -
316A ILE* 3.5 28.7 - - + -
317A PHE 2.8 8.4 + - - +
318A ILE* 3.4 20.0 - - + +
319A PHE* 2.8 26.3 + - - +
338A GLU* 5.1 3.1 - - - +
413A VAL* 1.3 71.9 - - - +
415A VAL* 1.3 63.8 + - - +
416A HIS* 4.7 0.9 - - - +
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Residues in contact with VAL 415 (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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281A ILE* 4.2 17.9 - - + -
282A THR 2.9 19.3 + - - +
283A ARG* 3.2 2.8 - - - -
284A CYS* 3.0 24.3 + - - -
319A PHE* 3.7 6.1 - - + +
402A ILE* 3.7 26.0 - - + -
413A VAL* 4.5 6.7 - - + -
414A VAL* 1.3 77.8 - - - +
416A HIS* 1.4 65.6 + - - +
424A THR* 3.7 16.6 - - + +
427A LEU* 3.9 36.6 - - + -
428A THR* 4.2 11.4 - - + +
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Residues in contact with HIS 416 (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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284A CYS* 3.1 31.2 - - - +
285A SER 4.0 4.7 - - - +
286A GLN* 4.0 10.3 - - - -
287A PRO* 4.2 4.8 - - + +
318A ILE* 3.4 22.3 - - + +
319A PHE 3.1 7.9 + - - +
320A ASP* 3.2 28.0 + - + -
321A ALA* 3.0 25.8 + - - +
322A ARG* 4.0 3.6 + - - -
336A GLY 4.7 0.4 + - - -
338A GLU* 3.0 37.9 + - - -
348A LEU* 4.6 0.2 - - + -
414A VAL* 4.7 0.8 - - - +
415A VAL* 1.4 78.0 - - - +
417A SER* 1.3 86.6 + - - +
424A THR* 2.9 15.4 + - - -
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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