Contacts of the strand formed by residues 308 - 312 (chain L) in PDB entry 6Y5D
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 308 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280L PHE* 3.8 11.4 - - + -
281L ARG* 3.9 20.9 - - + +
284L ILE* 3.8 24.7 - - + -
298L MET* 3.9 14.4 - - + -
301L LYS* 4.9 1.6 - - - -
306L PRO 4.4 1.6 - - - -
307L ALA* 1.3 86.3 + - - +
309L THR* 1.3 67.4 + - - +
310L LEU* 3.5 34.8 - - + -
318L VAL 3.7 0.9 - - - +
319L ASP* 3.9 0.2 - - - -
320L ILE* 2.9 43.2 + - + +
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Residues in contact with THR 309 (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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298L MET* 3.8 3.8 - - - +
299L LYS* 3.1 62.8 + - + +
301L LYS* 5.4 10.1 - - - +
306L PRO* 4.1 14.4 + - - +
308L VAL* 1.3 77.1 + - - +
310L LEU* 1.3 76.0 + - - +
311L LEU* 4.6 4.5 - - + -
317L SER* 5.5 3.4 - - - -
318L VAL 3.5 4.9 - - - +
319L ASP* 3.6 24.2 + - - +
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Residues in contact with LEU 310 (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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189L VAL* 3.9 16.8 - - + -
193L LEU* 3.7 30.3 - - + -
284L ILE* 4.2 4.0 - - + -
288L ILE* 4.2 6.7 - - + -
296L VAL* 4.0 21.1 - - + -
297L ILE 3.6 5.8 - - - +
298L MET* 4.1 15.0 - - + -
308L VAL* 3.5 26.2 - - + -
309L THR* 1.3 77.5 - - - +
311L LEU* 1.3 65.7 + - - +
312L ILE* 3.9 5.5 + - + -
317L SER* 3.5 4.2 - - - -
318L VAL* 3.0 44.1 + - + +
320L ILE* 3.7 14.4 - - + -
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Residues in contact with LEU 311 (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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295L ASP 3.6 2.1 - - - +
296L VAL* 3.4 3.5 - - - -
297L ILE* 2.8 61.0 + - + +
299L LYS* 4.3 40.8 - - + +
309L THR* 4.6 2.7 - - + -
310L LEU* 1.3 79.6 - - - +
312L ILE* 1.3 61.6 + - - +
313L SER 4.0 4.1 + - - +
316L ILE 3.9 2.7 - - - +
317L SER* 4.5 14.4 - - - -
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Residues in contact with ILE 312 (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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185L MET* 4.4 14.6 - - + -
186L VAL* 4.3 8.1 - - - -
189L VAL* 3.7 33.2 - - + -
294L THR* 3.6 23.3 - - + -
295L ASP 3.6 2.7 - - - -
296L VAL* 4.2 10.5 - - + -
310L LEU* 4.6 4.9 - - + +
311L LEU* 1.3 73.4 - - - +
313L SER* 1.3 74.8 + - - +
315L LYS 3.5 0.2 + - - -
316L ILE* 2.8 52.2 + - + +
318L VAL* 3.5 31.4 - - + -
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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