Contacts of the strand formed by residues 316 - 320 (chain B) in PDB entry 1TAD
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 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B SER* 5.1 7.6 - - - -
260B ILE 3.4 13.5 + - - -
261B VAL* 3.5 13.4 - - + -
262B LEU* 2.7 31.6 + - - +
314B GLU* 3.4 30.1 + - + +
315B ILE* 1.3 81.8 - - - +
317B SER* 1.3 55.7 + - - +
318B HIS* 4.8 5.2 - - - +
338B ILE* 3.5 56.0 - - + +
341B LYS* 5.9 3.1 - - - +
342B GLU 5.6 4.1 - - - -
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 3.3 14.0 + - - +
264B LEU* 3.5 15.4 - - - +
300B LYS* 3.2 36.6 + - - +
304B LEU* 4.4 16.6 - - - -
315B ILE 4.1 0.6 + - - -
316B TYR* 1.3 76.0 - - - +
318B HIS* 1.3 78.3 + - - +
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Residues in contact with HIS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B VAL* 3.9 24.7 - - + +
262B LEU 3.0 8.4 + - - +
263B PHE* 3.6 2.8 - - + -
264B LEU* 2.8 32.4 + - - +
300B LYS* 4.4 4.7 - - - +
316B TYR* 4.8 7.5 - - - +
317B SER* 1.3 92.8 + - - +
319B MET* 1.3 59.8 + - - +
320B THR* 3.6 7.0 + - + -
330B PHE* 5.2 7.9 - + - -
331B VAL* 3.7 35.2 - - + +
334B ALA* 3.9 27.2 - - + +
335B VAL* 4.7 4.0 - - + +
338B ILE* 4.9 5.1 - - - +
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Residues in contact with MET 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B LEU* 3.5 26.9 - - + -
264B LEU* 3.3 24.0 - - - +
267B LYS* 3.8 13.0 - - + +
270B PHE* 4.6 0.7 - - + -
292B TYR* 3.8 40.2 - - + +
296B GLY* 4.0 20.4 - - - +
300B LYS* 3.6 27.6 - - - +
318B HIS* 1.3 72.5 - - - +
320B THR* 1.3 63.5 + - - +
327B ASN* 4.0 8.1 + - - +
331B VAL* 4.6 2.3 - - - +
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 5.4 0.4 - - - +
263B PHE* 3.9 25.2 - - + +
264B LEU 2.7 11.1 + - - -
265B ASN* 3.0 28.1 + - - +
266B LYS 3.0 8.0 + - - -
267B LYS* 2.9 31.4 + - - +
318B HIS* 3.9 9.2 - - + +
319B MET* 1.3 79.7 - - - +
321B CYS* 1.3 63.2 + - - +
322B ALA* 4.5 1.7 - - - -
327B ASN* 3.3 11.2 - - - +
328B VAL* 5.7 3.8 - - + -
331B VAL* 4.0 28.7 - - + -
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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