Contacts of the strand formed by residues 454 - 460 (chain C) in PDB entry 2W4T
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 TYR 454 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C TYR* 3.2 21.7 + - - -
163C MET* 2.6 67.5 - - + -
164C VAL* 3.1 28.9 - - + +
167C ARG* 5.6 1.8 - - - -
168C GLU* 4.0 15.0 - - - +
169C ASN* 3.6 13.7 - - - +
250C HIS* 3.7 3.3 - - - +
251C PHE* 2.9 45.6 + + + +
252C GLY 5.1 4.0 - - - -
255C GLY* 4.7 3.6 - - - -
453C ASN* 1.3 90.4 + - + +
455C TYR* 1.3 68.1 + - - +
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Residues in contact with TYR 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C MET* 2.6 29.9 - - - +
169C ASN* 2.9 44.6 + - + +
170C GLN 3.1 10.2 + - - -
248C ARG* 0.5 80.8 + - + +
249C ILE 3.3 22.4 - - - +
250C HIS* 3.9 20.6 - + + +
251C PHE* 4.3 0.2 - - - -
454C TYR* 1.3 81.6 - - - +
456C ILE* 1.3 57.5 + - - +
457C GLY 3.6 0.2 - - - -
659C ASN* 4.4 13.2 + - - +
662C SER* 4.5 5.2 + - - -
663C THR* 4.6 1.4 - - - +
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Residues in contact with ILE 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ALA* 4.9 4.0 - - + -
160C TYR 6.1 0.2 - - - +
163C MET* 3.3 15.5 - - + -
170C GLN* 3.3 10.3 - - + -
171C SER* 3.3 30.5 - - - +
172C CYS* 4.3 1.1 - - - +
189C VAL* 5.9 4.7 - - + -
192C TYR* 5.7 4.0 - - - +
193C LEU* 3.3 9.0 - - + -
249C ILE* 2.3 71.3 + - + +
251C PHE* 3.2 7.9 - - + -
455C TYR* 1.3 76.3 - - - +
457C GLY* 1.3 70.3 + - - +
458C VAL* 4.4 7.0 - - + +
666C HIS* 3.6 13.9 - - + -
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Residues in contact with GLY 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLN 3.6 1.4 + - - -
171C SER* 3.6 1.5 - - - -
172C CYS 3.3 19.7 + - - -
246C PHE* 4.2 3.4 - - - -
247C ILE 3.3 2.9 - - - -
248C ARG* 3.2 46.5 - - - +
456C ILE* 1.3 76.8 - - - +
458C VAL* 1.3 70.5 + - - +
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Residues in contact with VAL 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C CYS* 3.2 27.4 - - - -
174C ILE* 4.3 5.6 - - + -
186C THR* 3.9 31.9 - - + +
189C VAL* 4.3 16.6 - - + -
190C ILE* 4.9 6.1 - - + -
245C LYS 3.7 0.7 - - - +
246C PHE* 3.5 5.4 - - - -
247C ILE* 2.9 54.7 + - + +
249C ILE* 5.1 3.8 - - + -
456C ILE* 4.4 9.9 - - + +
457C GLY* 1.3 81.3 - - - +
459C LEU* 1.3 63.9 + - - +
460C ASP* 5.5 0.2 - - - +
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C CYS 3.0 7.8 + - - +
173C LEU* 2.7 37.4 - - + +
174C ILE* 3.4 29.9 + - - +
245C LYS 3.6 4.3 - - - +
246C PHE* 2.4 60.8 - - + -
458C VAL* 1.3 72.5 - - - +
460C ASP* 1.3 59.0 + - - +
461C ILE* 3.9 21.2 + - + +
483C ARG* 6.0 3.1 - - - +
656C LEU* 4.9 12.1 - - + +
660C LEU* 3.1 28.5 - - + -
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Residues in contact with ASP 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ILE* 4.3 6.3 - - + -
182C LYS* 4.9 9.2 - - + +
183C THR* 5.2 8.3 - - + +
186C THR* 3.6 29.4 - - + +
241C SER* 4.7 3.1 + - - -
243C PHE 4.5 3.3 - - - +
244C GLY* 4.0 0.5 - - - -
245C LYS* 2.2 80.9 + - - +
247C ILE* 4.6 8.0 - - - +
458C VAL 4.3 3.3 - - - +
459C LEU* 1.3 72.2 - - - +
461C ILE* 1.3 59.7 + - - +
462C ALA* 3.8 3.7 + - - -
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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