Contacts of the strand formed by residues 302 - 307 (chain L) in PDB entry 6R8Y
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 302 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K ARG* 3.7 42.0 - - - +
137K ASP* 2.9 32.5 + - - -
296L PHE* 3.8 1.6 - - - -
297L SER* 3.1 33.3 + - - -
300L GLY 5.2 0.9 - - - -
301L ALA* 1.3 83.7 + - - +
303L LEU* 1.3 61.0 + - - +
314L VAL* 4.2 20.6 - - + -
315L TYR 3.7 2.9 - - - +
316L SER* 2.7 33.5 + - - -
317L ALA* 5.4 0.4 - - - +
324L LEU* 3.8 19.3 - - - +
344L TRP* 3.9 23.5 - - + -
349L ASN* 4.7 7.0 - - - +
377L GLY 6.1 1.1 - - - -
378L ASN* 4.9 19.1 - - - +
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Residues in contact with LEU 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259L ALA* 5.1 2.2 - - + -
267L VAL* 5.6 2.9 - - + -
269L ILE* 4.0 26.5 - - + -
285L LEU* 4.9 4.9 - - + -
294L ALA* 4.4 9.2 - - + -
295L CYS 3.3 30.1 - - - +
296L PHE* 4.0 26.0 - - + +
301L ALA 4.1 1.6 + - - -
302L ARG* 1.3 72.3 - - - +
304L LEU* 1.3 69.0 + - - +
305L THR* 4.2 10.5 - - - +
313L ARG 4.0 0.2 - - - +
314L VAL* 3.7 4.5 - - - +
315L TYR* 2.8 54.0 + - + +
316L SER* 4.9 0.2 - - - +
320L TRP* 4.6 17.0 - - + -
344L TRP* 4.6 1.1 - - - -
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Residues in contact with LEU 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293L ALA 4.1 0.2 - - - +
294L ALA* 3.3 2.6 - - - -
295L CYS* 2.9 37.1 + - + +
302L ARG 4.0 0.6 + - - -
303L LEU* 1.3 73.3 - - - +
305L THR* 1.3 70.5 + - - +
306L THR* 5.6 0.9 - - + -
312L ILE* 3.9 14.4 - - + -
313L ARG 3.7 12.8 - - - +
314L VAL* 4.3 6.7 - - + -
342L ALA* 3.4 34.8 - - + +
343L ALA* 4.2 11.2 - - - +
344L TRP* 3.5 26.5 - - + +
351L ILE* 3.5 37.7 - - + -
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Residues in contact with THR 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L VAL* 4.9 5.2 - - + +
287L HIS* 3.5 35.0 - - + +
291L VAL* 4.0 11.9 - - + -
293L ALA 3.4 11.4 - - - +
294L ALA* 4.3 9.4 - - + +
303L LEU* 4.2 8.0 - - - +
304L LEU* 1.3 80.1 + - - +
306L THR* 1.3 66.6 + - - +
312L ILE* 3.4 6.8 - - - +
313L ARG* 2.9 37.8 + - - +
315L TYR* 3.8 20.8 - - - -
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Residues in contact with THR 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291L VAL* 3.8 2.3 - - - -
292L ASN* 2.9 23.2 + - - -
293L ALA* 2.9 40.3 + - + +
304L LEU* 5.6 0.7 - - + -
305L THR* 1.3 81.6 - - - +
307L ASP* 1.3 61.8 + - - +
311L GLU 4.1 4.7 - - - -
312L ILE* 4.1 12.2 - - - +
331L HIS* 3.2 21.1 + - - -
340L ILE* 4.3 10.8 + - - +
342L ALA* 4.0 27.0 + - + +
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Residues in contact with ASP 307 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287L HIS* 5.3 7.0 - - + +
289L HIS* 4.1 9.2 + - + +
290L PRO 3.4 17.3 - - - +
291L VAL* 4.1 4.9 - - + +
292L ASN* 3.0 13.8 - - - +
306L THR* 1.3 77.1 + - - +
308L GLN* 1.3 56.8 + - - +
309L LYS* 2.5 28.9 + - - +
310L SER 2.9 9.0 + - - -
311L GLU* 2.5 55.7 + - + +
313L ARG* 6.2 0.4 - - - +
331L HIS* 2.9 25.9 + - - -
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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