Contacts of the strand formed by residues 307 - 311 (chain A) in PDB entry 4X2Q
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 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A LYS* 3.0 58.3 - - + +
273A SER 3.6 4.7 - - - +
274A PRO* 3.4 17.4 - - + +
275A ASN* 2.9 22.5 + - - +
306A SER* 1.3 81.6 + - - +
308A ILE* 1.3 61.3 + - - +
309A PHE* 3.2 40.1 - - + -
391A ASP* 4.3 15.0 + - - +
396A ALA* 3.4 39.5 + - - +
399A GLU* 4.9 3.4 - - - +
406A GLU* 4.3 11.0 - - + +
408A LEU* 4.2 22.3 - - + +
419A ARG 4.0 1.4 + - - -
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Residues in contact with ILE 308 (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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275A ASN* 3.4 23.1 - - + +
277A ILE* 3.8 28.5 - - + -
290A ALA* 3.9 19.1 - - + +
294A VAL* 3.8 20.2 - - + -
306A SER 3.7 6.3 - - - +
307A ARG* 1.3 80.1 - - - +
309A PHE* 1.3 64.8 + - - +
310A VAL* 3.9 13.9 + - + +
318A PHE* 4.3 5.4 - - + -
405A GLN* 3.5 28.9 - - - +
406A GLU 3.3 11.5 + - - +
407A ILE* 3.7 2.1 - - + -
408A LEU* 2.9 29.0 + - - +
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Residues in contact with PHE 309 (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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274A PRO* 3.9 17.0 - - + -
275A ASN 2.7 20.2 + - - +
276A ILE* 4.4 6.3 - - + -
277A ILE* 2.8 30.8 + - - +
307A ARG* 3.2 42.8 - - + -
308A ILE* 1.3 73.5 - - - +
310A VAL* 1.3 61.3 + - - +
391A ASP* 4.4 0.7 - - - -
408A LEU* 3.6 25.8 - - + -
410A PHE* 3.6 17.1 - - + -
416A VAL* 3.7 16.8 - - + -
419A ARG* 3.2 52.5 - - + -
420A ALA* 4.2 8.5 - - + -
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.7 6.5 - - + +
308A ILE* 4.0 11.2 - - + +
309A PHE* 1.3 77.0 - - - +
311A GLU* 1.3 70.7 + - - +
312A GLU 3.6 0.2 + - - -
314A ILE* 3.8 27.4 - - + -
315A TYR* 3.8 15.7 - - + -
318A PHE* 3.6 53.4 - - + -
407A ILE* 4.0 10.8 - - + -
408A LEU 2.9 18.6 + - - +
409A ARG* 3.7 3.3 - - - -
410A PHE* 3.4 16.2 + - - -
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Residues in contact with GLU 311 (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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277A ILE 3.2 16.2 + - - +
278A PHE* 3.4 20.9 - - - -
279A ALA* 2.8 44.4 + - + +
310A VAL* 1.3 74.6 - - - +
312A GLU* 1.3 69.6 + - + +
313A SER* 3.0 13.6 + - - +
314A ILE* 3.1 8.1 + - + +
315A TYR* 3.0 19.8 + - - +
410A PHE* 3.3 25.5 - - + +
411A LYS 4.5 9.9 - - - +
438A LYS* 4.5 9.6 + - - -
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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