Contacts of the strand formed by residues 360 - 368 (chain A) in PDB entry 4PHZ
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 ALA 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A VAL 3.2 11.4 - - - +
307A LYS* 3.8 18.2 - - + -
358A GLY 3.7 2.0 + - - +
359A GLU* 1.3 78.8 + - - +
361A LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 361 (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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304A VAL 3.3 2.8 - - - +
305A LYS* 4.5 1.3 - - - -
306A VAL* 2.8 39.8 + - - +
350A VAL* 5.1 4.4 - - - +
351A ASP* 5.5 4.6 - - - +
353A THR* 3.5 41.4 + - - +
355A ILE* 4.4 15.7 - - + +
359A GLU* 3.8 30.1 + - + +
360A ALA* 1.3 75.3 - - - +
362A GLU* 1.3 64.6 + - - +
363A ILE* 3.6 23.1 + - + +
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Residues in contact with GLU 362 (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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289A ASN* 3.2 24.2 + - - -
303A ASN* 3.4 26.6 + - + +
304A VAL 3.3 11.4 - - - +
305A LYS* 3.3 33.8 - - + +
361A LYS* 1.3 76.4 - - - +
363A ILE* 1.3 63.2 + - - +
364A VAL* 4.4 1.8 + - + +
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Residues in contact with ILE 363 (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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302A ILE 3.6 0.9 - - - +
303A ASN* 3.4 2.2 - - - -
304A VAL* 2.8 40.1 + - + +
306A VAL* 3.4 25.6 - - + -
316A LEU* 4.4 15.5 - - + -
349A SER 5.8 0.7 - - - +
350A VAL* 5.1 19.5 - - + -
355A ILE* 5.2 6.7 - - + -
361A LYS* 3.7 35.4 - - + +
362A GLU* 1.3 79.0 - - - +
364A VAL* 1.3 63.3 + - - +
365A VAL* 3.7 22.4 + - + -
394A PHE* 4.7 5.8 - - + -
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Residues in contact with VAL 364 (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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301A THR* 4.0 23.6 - - + -
302A ILE 3.5 3.8 - - - -
303A ASN* 3.7 17.5 - - + +
349A SER 3.3 17.8 - - - +
362A GLU* 5.8 1.1 - - + +
363A ILE* 1.3 73.9 - - - +
365A VAL* 1.3 66.1 + - - +
366A LYS* 4.3 5.2 + - + +
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Residues in contact with VAL 365 (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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300A LEU 3.6 1.6 - - - +
301A THR* 3.4 2.5 - - - -
302A ILE* 2.6 56.5 + - + +
304A VAL* 4.2 10.8 - - + -
316A LEU* 3.7 26.0 - - + -
319A TYR* 6.1 1.8 - - + -
347A GLY 4.2 18.4 - - - +
349A SER 4.4 10.3 - - - +
350A VAL* 6.2 0.2 - - - -
363A ILE* 3.7 22.9 - - + +
364A VAL* 1.3 79.4 - - - +
366A LYS* 1.3 62.2 + - - +
367A ILE* 3.8 17.0 + - + -
392A LEU* 5.7 3.6 - - + -
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Residues in contact with LYS 366 (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 GLU* 3.7 19.2 + - + +
300A LEU 3.6 2.7 - - - +
301A THR* 4.2 18.4 - - + +
346A ARG* 4.1 9.6 - - - +
348A LEU* 2.7 50.3 + - + +
349A SER 4.2 1.5 - - - +
364A VAL* 4.2 5.3 + - + -
365A VAL* 1.3 75.6 - - - +
367A ILE* 1.3 63.0 + - - +
368A GLN* 2.9 45.1 + - - +
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Residues in contact with ILE 367 (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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298A ARG 5.3 0.9 - - - +
299A GLU* 3.3 4.7 - - - +
300A LEU* 2.6 73.2 + - + +
302A ILE* 4.0 25.4 - - + -
319A TYR* 4.0 24.0 - - + -
326A PHE* 3.4 39.7 - - + -
346A ARG 3.9 2.5 - - - -
347A GLY* 4.8 9.9 - - - -
365A VAL* 4.1 13.9 - - + +
366A LYS* 1.3 72.4 - - - +
368A GLN* 1.3 65.1 + - - +
369A ASP 5.1 0.2 - - - +
372A TRP* 4.9 8.5 - - + -
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Residues in contact with GLN 368 (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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298A ARG* 3.4 23.7 - - - +
299A GLU* 3.4 26.3 + - + +
346A ARG* 3.0 65.7 + - - +
366A LYS* 2.9 37.8 + - - +
367A ILE* 1.3 78.9 - - - +
369A ASP* 1.3 68.4 + - - +
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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