Contacts of the strand formed by residues 333 - 337 (chain R) 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 VAL 333 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325R ALA* 5.4 0.7 - - + -
326R SER 3.4 12.8 - - - +
332R LEU* 1.3 74.8 - - - +
334R ASN* 1.3 68.8 + - - +
349R GLN 3.9 0.2 - - - +
350R THR* 3.3 5.5 - - - +
351R PHE* 2.8 66.7 + - + +
354R HIS* 3.6 32.8 - - + +
358R VAL* 3.8 18.6 - - + -
361R VAL* 5.3 2.0 - - + -
371R LEU* 4.7 6.1 - - + -
373R THR* 3.9 21.8 - - + +
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Residues in contact with ASN 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307R GLY* 2.9 35.0 + - - -
308R HIS* 3.3 19.4 + - - -
324R LEU 3.9 0.7 - - - +
325R ALA* 3.3 4.0 - - - +
326R SER* 2.8 48.1 + - - +
332R LEU* 3.8 4.8 - - - +
333R VAL* 1.3 73.8 - - - +
335R VAL* 1.3 63.3 + - - +
336R TRP* 3.5 12.9 - - + +
347R PRO* 3.7 13.6 - - + +
349R GLN 3.4 2.2 - - - +
350R THR* 3.0 34.5 + - - +
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Residues in contact with VAL 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323R HIS* 3.9 37.5 - - + -
324R LEU 3.5 4.7 - - - +
325R ALA* 4.6 1.8 - - + -
333R VAL* 5.1 0.7 - - + -
334R ASN* 1.3 76.0 - - - +
336R TRP* 1.3 57.3 + - - +
347R PRO* 3.5 2.0 - - - +
348R LEU* 2.8 34.6 + - + +
349R GLN* 2.9 28.5 + - + +
351R PHE* 3.8 28.5 - - + -
363R TRP* 4.2 8.3 - - + -
371R LEU* 4.0 17.7 - - + -
387R VAL* 4.2 11.7 - - + +
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Residues in contact with TRP 336 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290R ILE* 3.8 16.7 - - + +
305R LEU* 3.6 37.0 - - + -
306R SER 3.7 10.8 - - - -
307R GLY* 3.5 34.3 - - - -
323R HIS* 3.5 10.2 - - - +
324R LEU* 2.7 53.4 + - + +
326R SER* 2.9 31.4 + - - -
334R ASN* 3.5 16.0 - - + +
335R VAL* 1.3 74.2 - - - +
337R PRO* 1.4 72.5 - - + +
345R TRP* 3.6 25.4 - + + -
346R VAL 4.1 4.7 - - - -
347R PRO* 3.6 35.2 - - + -
348R LEU* 4.2 2.9 - - - -
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Residues in contact with PRO 337 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292R HIS* 5.0 0.7 + - - -
317R TRP* 4.5 7.5 - - - -
322R ARG 4.3 3.8 - - - +
324R LEU* 5.2 0.2 - - - +
336R TRP* 1.4 95.4 - - + +
338R SER* 1.3 59.6 + - - +
339R ALA 3.4 22.0 - - - +
340R PRO* 4.8 0.2 - - + -
341R GLY* 4.7 10.3 - - - +
345R TRP* 3.3 27.8 - - + -
346R VAL 3.5 24.7 - - - +
348R LEU* 3.8 32.7 - - + -
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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
------------------------------------------------------------
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