Contacts of the strand formed by residues 315 - 320 (chain I) 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 ARG 315 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313I PRO 5.7 0.2 - - - +
314I LEU* 1.3 77.6 - - - +
316I LEU* 1.3 61.1 + - - +
317I GLY 3.4 0.9 + - - -
330I ASP* 3.8 16.8 + - - +
331I VAL* 3.6 42.6 + - + +
350I VAL* 4.6 9.9 - - + -
352I ALA* 3.7 33.9 - - - +
354I PRO* 3.9 14.6 - - + -
355I ILE* 5.1 0.2 - - - -
394I PHE* 3.4 3.1 - - - -
395I PHE* 2.7 47.8 + - - +
396I SER 3.0 27.3 + - - -
397I PRO* 4.4 11.2 + - - +
398I ASP 5.0 0.6 + - - -
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Residues in contact with LEU 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314I LEU 4.3 0.2 + - - -
315I ARG* 1.3 70.8 - - - +
317I GLY* 1.3 57.5 + - - +
318I GLU 3.5 26.2 - - - +
328I ASN* 3.0 27.9 + - - +
331I VAL* 4.0 1.6 - - - +
347I GLY 5.5 4.5 - - - +
349I SER 6.0 0.4 - - - -
350I VAL* 3.5 20.6 - - + +
355I ILE* 5.3 0.4 - - - +
363I ILE* 4.3 12.6 - - + -
365I VAL* 3.7 35.7 - - + -
392I LEU* 3.8 31.6 - - + -
393I PHE 3.5 9.6 - - - +
394I PHE* 3.5 27.7 - - + -
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Residues in contact with GLY 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315I ARG 3.4 4.4 + - - -
316I LEU* 1.3 73.5 - - - +
318I GLU* 1.3 59.4 - - - +
327I LEU* 3.4 0.9 - - - -
328I ASN* 2.7 29.9 + - - -
331I VAL* 3.8 17.3 - - - -
332I PHE* 3.2 13.9 - - - -
347I GLY 5.7 1.3 - - - -
393I PHE 2.8 8.1 + - - -
395I PHE* 3.6 17.7 - - - -
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Residues in contact with GLU 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316I LEU* 3.5 13.5 - - - +
317I GLY* 1.3 80.4 - - - +
319I TYR* 1.3 67.6 + - - +
320I THR* 3.0 17.3 + - - -
325I ARG* 2.6 49.0 + - - +
326I PHE 3.3 6.7 - - - +
327I LEU* 3.4 13.5 - - + -
332I PHE* 3.6 13.9 - - + -
347I GLY 5.8 2.0 - - - -
392I LEU* 3.5 1.4 - - - -
393I PHE* 2.8 59.8 + - + +
395I PHE* 4.8 1.0 - - - -
401I ARG* 5.8 1.6 + - - -
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Residues in contact with TYR 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I MET* 4.5 1.6 - - - -
300I LEU* 4.8 8.0 - - + +
302I ILE* 5.6 1.8 - - + -
318I GLU* 1.3 75.1 - - - +
320I THR* 1.3 67.8 + - - +
321I ALA* 4.0 20.7 - - + +
326I PHE* 2.8 63.0 + + + +
347I GLY 5.6 3.8 - - - +
365I VAL* 6.2 2.2 - - + -
367I ILE* 4.0 27.8 - - + -
372I TRP* 5.2 3.4 - + - -
388I ILE* 3.9 22.2 - - + +
389I GLY 3.1 20.6 + - - -
390I GLY* 4.5 0.2 - - - -
391I LEU 3.4 15.0 - - - -
392I LEU* 3.6 19.3 - - + -
406I ILE* 3.7 22.0 - - + -
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Residues in contact with THR 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ASN* 5.1 3.8 - - + +
45I TRP 3.2 30.2 + - - +
46I TYR* 5.3 1.7 - - - +
318I GLU* 3.0 27.0 + - - +
319I TYR* 1.3 75.2 - - - +
321I ALA* 1.3 65.8 + - - +
323I GLY 4.1 16.8 - - - +
324I LEU 3.1 9.2 - - - +
325I ARG* 3.5 9.6 - - + +
390I GLY* 3.6 4.9 - - - -
391I LEU* 3.1 35.2 + - + +
393I PHE* 4.2 13.9 - - - -
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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