Contacts of the strand formed by residues 254 - 259 (chain A) in PDB entry 3F9B
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 THR 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE 3.6 1.6 - - - +
250A GLN* 3.2 2.9 - - - -
251A VAL* 2.9 37.4 + - - +
253A ASN* 1.3 75.7 - - - +
255A ARG* 1.3 62.9 + - - +
256A THR* 4.0 17.7 + - + +
373A ASP* 5.9 0.9 - - - +
414A ILE* 5.6 3.3 - - + +
417A MET* 4.7 12.8 - - + +
418A CYS* 3.6 20.3 - - + +
421A ASP* 2.7 26.6 + - + +
423A ARG* 4.2 1.8 - - - +
424A ASN* 2.8 17.3 + - - -
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE 3.4 3.8 - - - -
250A GLN* 3.1 36.3 + - + +
253A ASN* 2.8 34.6 + - - +
254A THR* 1.3 74.7 - - - +
256A THR* 1.3 69.5 + - - +
380A ARG* 5.8 0.2 + - - -
394A ASP* 2.6 34.4 + - - +
398A ARG* 3.6 31.5 - - + +
399A PRO* 3.4 16.6 - - - +
423A ARG* 4.0 14.8 - - - +
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Residues in contact with THR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 2.9 39.5 + - - +
254A THR* 4.5 14.4 + - + +
255A ARG* 1.3 79.2 - - - +
257A ILE* 1.3 64.2 + - - +
398A ARG* 3.0 15.6 + - - -
399A PRO* 3.5 21.1 - - + +
401A ILE* 3.7 20.9 - - + -
414A ILE* 3.8 28.6 - - + +
417A MET* 4.3 13.2 - - + -
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Residues in contact with ILE 257 (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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240A VAL* 4.0 23.8 - - + -
246A ALA* 4.4 2.2 - - + -
247A ASN 3.2 10.5 - - - +
248A TYR* 3.9 32.1 - - + -
256A THR* 1.3 80.0 - - - +
258A ALA* 1.3 70.4 + - - +
259A CYS* 4.7 0.2 - - + -
273A MET* 4.3 15.9 - - + -
277A ASN* 4.0 35.0 - - + +
398A ARG* 3.9 5.2 - - + -
399A PRO 2.8 10.4 + - - +
400A VAL* 3.4 17.8 - - + -
401A ILE* 2.9 30.1 + - - +
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Residues in contact with ALA 258 (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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246A ALA* 3.4 1.0 - - - -
247A ASN* 2.8 31.3 + - - -
249A ILE* 3.7 27.5 - - + +
256A THR 4.3 0.4 - - - -
257A ILE* 1.3 73.9 - - - +
259A CYS* 1.3 61.1 + - - +
401A ILE 3.4 5.2 - - - -
410A THR* 3.9 11.4 - - + -
414A ILE* 3.8 17.7 - - + -
440A ARG* 3.7 18.1 + - - +
444A MET* 4.3 1.3 - - + -
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Residues in contact with CYS 259 (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 ASN 3.3 14.6 - - - +
246A ALA* 3.5 15.3 - - + +
257A ILE* 4.7 1.3 - - + -
258A ALA* 1.3 77.1 - - - +
260A GLN* 1.3 73.6 + - - +
270A HIS* 4.0 13.0 - - - +
273A MET* 4.5 2.7 - - + -
400A VAL* 4.0 21.3 - - - -
401A ILE 3.1 6.9 + - - -
402A HIS* 2.9 42.4 - - - +
406A GLY* 3.2 13.3 - - - -
440A ARG* 3.6 8.5 - - - +
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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