Contacts of the strand formed by residues 305 - 310 (chain C) in PDB entry 1TYE
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 ASP 305 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C PHE* 4.7 1.8 - - - -
295C VAL* 3.4 9.3 - - - +
296C THR* 2.8 38.8 + - - +
297C ASP* 2.8 12.1 - - - +
298C VAL* 2.9 23.6 + - + +
299C ASN* 2.9 3.3 - - - +
304C HIS* 1.3 75.2 - - - +
306C LEU* 1.3 61.5 + - - +
307C LEU* 5.4 0.6 - - - +
330C LEU* 4.4 4.0 - - + -
331C PHE 3.7 7.6 - - - +
332C LEU* 3.4 17.1 - - + +
333C GLN 3.1 22.9 + - - -
1412C CA 2.2 32.0 - - - -
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Residues in contact with LEU 306 (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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244C PHE* 4.7 6.2 - - + -
254C VAL* 3.9 24.7 - - + -
267C VAL* 4.6 1.6 - - + -
269C ILE* 3.8 23.1 - - + -
280C LEU* 3.5 30.7 - - + -
293C VAL* 4.8 0.9 - - + -
294C ALA 3.4 15.7 - - - +
295C VAL* 4.4 7.9 - - + -
305C ASP* 1.3 74.1 - - - +
307C LEU* 1.3 75.1 + - - +
308C VAL* 4.2 13.2 - - + -
330C LEU* 3.3 8.5 - - - +
331C PHE* 2.8 48.5 + - + +
340C LEU* 4.3 11.0 - - + -
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C SER 3.8 0.2 - - - +
293C VAL* 3.3 6.2 - - - -
294C ALA* 3.0 39.6 + - + +
296C THR* 4.4 13.2 - - + -
298C VAL* 5.0 2.0 - - + -
305C ASP* 5.4 1.1 - - + +
306C LEU* 1.3 77.0 - - - +
308C VAL* 1.3 63.3 + - - +
328C VAL* 4.1 10.1 - - + -
329C TYR 3.2 12.8 - - - +
330C LEU* 3.7 28.3 - - + -
360C ILE* 3.7 28.7 - - + +
362C PRO* 6.0 0.4 - - + -
374C ILE* 3.5 45.5 - - + -
399C LEU* 4.2 4.9 - - + -
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Residues in contact with VAL 308 (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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267C VAL* 3.6 27.4 - - + -
280C LEU* 4.8 0.7 - - + -
289C PHE* 3.7 24.2 - - + -
290C GLY* 3.4 28.3 - - - +
292C SER 3.4 4.5 - - - +
293C VAL* 4.7 1.8 - - + -
306C LEU* 4.2 17.0 - - + -
307C LEU* 1.3 79.2 - - - +
309C GLY* 1.3 60.8 + - - +
328C VAL* 3.3 6.1 - - - +
329C TYR* 2.9 34.4 + - + +
331C PHE* 4.1 20.2 - - + -
360C ILE* 3.9 3.1 - - - -
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Residues in contact with GLY 309 (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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288C TYR 3.2 13.5 - - - +
290C GLY 3.3 12.2 + - - -
291C HIS 3.4 6.6 + - - -
292C SER 2.8 14.7 + - - -
308C VAL* 1.3 74.8 - - - +
310C ALA* 1.3 58.2 + - - -
311C PRO* 3.5 8.1 - - - +
327C ARG 3.7 4.5 - - - -
328C VAL* 4.6 0.2 - - - -
357C GLY* 3.2 21.3 - - - -
360C ILE* 3.8 7.2 - - - +
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Residues in contact with ALA 310 (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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287C SER* 3.3 23.6 - - - +
288C TYR 3.7 2.5 - - - -
289C PHE* 3.8 15.9 - - + -
309C GLY* 1.3 70.0 - - - -
311C PRO* 1.3 63.9 - - - +
312C LEU 2.9 10.1 + - - -
313C TYR* 3.1 13.7 + - + -
327C ARG 2.8 27.8 + - - +
329C TYR* 4.0 18.8 - - + +
357C GLY 4.0 0.4 + - - -
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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