Contacts of the strand formed by residues 243 - 249 (chain A) in PDB entry 6KSF
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 LEU 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ASP* 4.4 4.9 - - - +
242A PRO* 1.3 74.0 - - - +
244A LEU* 1.3 75.0 + - - +
245A SER* 4.4 6.5 - - - -
276A MET 3.6 0.7 - - - +
277A VAL* 3.3 5.2 - - - -
278A MET* 2.8 55.3 + - + +
283A ARG* 3.7 31.4 - - - +
342A THR* 4.1 13.2 - - + -
343A VAL 3.4 10.1 - - - +
344A ARG* 3.4 44.2 - - + +
401A CL 4.2 0.4 - - + -
403A SIN 4.6 7.0 - - + +
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Residues in contact with LEU 244 (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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200A SER* 3.3 41.3 - - - +
203A VAL* 3.8 21.1 - - + -
204A ALA* 4.3 3.8 - - + +
212A PHE* 3.7 29.6 - - + -
242A PRO* 4.0 18.8 - - + +
243A LEU* 1.3 80.1 - - - +
245A SER* 1.3 61.6 + - - +
246A PHE* 3.9 17.3 - - + -
275A ILE* 5.2 1.1 - - + -
276A MET 3.5 3.8 - - - +
277A VAL* 4.5 12.3 - - + -
341A MET 3.5 1.0 - - - +
342A THR* 3.2 7.4 - - - +
343A VAL* 2.9 38.0 + - + +
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Residues in contact with SER 245 (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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243A LEU* 4.4 11.7 - - - -
244A LEU* 1.3 75.6 - - - +
246A PHE* 1.3 60.7 + - - +
247A SER 4.3 0.2 + - - -
270A MET* 5.6 3.1 - - - -
274A ASP 3.9 0.9 - - - +
275A ILE* 3.4 4.7 - - - +
276A MET* 2.9 55.5 + - - +
278A MET* 5.3 4.9 - - - -
340A ASN* 3.2 27.1 + - - -
341A MET 3.1 4.3 - - - -
342A THR* 4.1 3.4 + - - -
403A SIN 5.7 2.7 - - - +
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Residues in contact with PHE 246 (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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106A PHE* 4.2 11.2 - + - -
196A LEU* 4.9 0.4 - - + -
199A LEU* 3.8 28.0 - - + -
200A SER* 4.2 11.4 - - - -
203A VAL* 4.1 9.6 - - + -
244A LEU* 3.9 38.4 - - + -
245A SER* 1.3 75.1 - - - +
247A SER* 1.3 60.6 + - - +
248A PHE* 4.1 9.2 - - + -
273A GLY 6.3 0.2 - - - -
274A ASP 3.8 4.5 - - - +
275A ILE* 3.5 35.9 - - + -
339A VAL 3.8 0.2 - - - +
340A ASN* 3.1 10.0 - - - +
341A MET* 2.8 71.3 + - + +
343A VAL* 4.6 5.4 - - + -
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Residues in contact with SER 247 (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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245A SER 4.3 0.4 + - - -
246A PHE* 1.3 74.6 - - - +
248A PHE* 1.3 63.3 + - - +
250A GLN 4.7 1.6 + - - -
270A MET* 4.5 17.8 + - - +
271A HIS 4.3 10.2 + - - -
272A SER* 4.5 1.5 - - - -
273A GLY* 2.7 32.6 + - - -
274A ASP* 3.3 13.0 + - - -
338A ARG* 2.7 40.3 + - - +
339A VAL 3.4 3.6 - - - -
340A ASN* 4.0 2.2 - - - -
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Residues in contact with PHE 248 (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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106A PHE* 4.0 34.5 - + - -
111A GLN* 3.8 34.1 - - + -
114A TRP* 3.8 22.7 - - + -
115A VAL* 3.5 29.6 - - + -
118A CYS* 5.1 0.9 - - - -
246A PHE* 4.1 9.9 - - + -
247A SER* 1.3 83.2 + - - +
249A GLY* 1.3 60.3 + - - +
272A SER* 3.7 4.5 - - - +
273A GLY* 4.1 0.9 - - - -
334A LEU* 4.9 1.1 - - - -
338A ARG* 3.5 7.2 - - - +
339A VAL* 2.9 49.4 + - + +
341A MET* 3.6 37.7 - - + -
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Residues in contact with GLY 249 (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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248A PHE* 1.3 72.1 - - - +
250A GLN* 1.3 69.1 + - - +
251A SER 3.7 0.3 + - - -
272A SER* 3.0 21.3 + - - -
302A PRO* 3.3 23.9 - - - +
305A LEU* 4.1 16.3 - - - +
334A LEU* 4.3 13.7 - - - +
337A ALA 4.0 5.2 - - - -
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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