Contacts of the strand formed by residues 303 - 308 (chain C) in PDB entry 2Y1M
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 TRP 303 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ARG 5.6 0.7 - - - -
247C LEU* 3.1 44.2 + - + +
248C PHE* 3.7 37.0 - + - -
261C LEU* 5.4 1.8 - - + -
268C TYR* 3.7 27.4 - + - -
293C PHE* 3.9 16.2 - + + -
294C ARG 3.6 11.0 - - - -
295C LEU* 3.2 32.5 - - + -
301C GLY 5.4 0.7 - - - -
302C GLN* 1.3 75.4 - - - +
304C ALA* 1.3 63.2 + - - +
305C ILE* 5.2 0.7 - - + -
318C ILE* 3.4 26.0 - - - +
319C PRO* 3.6 24.6 + - + +
322C LYS 6.2 0.2 - - - -
324C LEU* 3.3 46.1 - - + +
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Residues in contact with ALA 304 (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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392B LYS* 6.2 0.9 - - - +
293C PHE* 3.5 3.1 - - - +
294C ARG* 2.9 52.9 + - + +
295C LEU 6.2 0.2 - - - -
296C SER* 6.0 2.7 - - - -
303C TRP* 1.3 76.0 - - - +
305C ILE* 1.3 63.2 + - - +
306C GLY 4.1 1.0 + - - -
316C GLN* 3.9 24.0 - - + +
317C THR 3.3 10.1 - - - +
318C ILE* 4.5 10.5 - - + -
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C TYR* 4.2 13.0 - - + -
292C ILE 3.6 12.1 - - - +
293C PHE* 4.0 11.9 - - + -
303C TRP* 5.2 0.4 - - + -
304C ALA* 1.3 77.2 - - - +
306C GLY* 1.3 68.6 + - - +
307C TYR* 4.1 3.6 - - - -
315C LEU 3.8 0.2 - - - +
316C GLN* 3.2 5.9 - - - -
317C THR* 2.8 39.3 + - + +
319C PRO* 4.3 19.7 - - + -
324C LEU* 4.0 23.8 - - + -
327C ALA* 4.5 7.2 - - + -
328C LEU* 4.2 7.4 - - + -
337C TYR* 3.9 45.3 - - + +
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Residues in contact with GLY 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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277C VAL* 4.2 13.9 - - - +
281C LEU* 3.9 17.0 - - - -
291C TYR* 3.1 25.1 - - - +
292C ILE 3.0 13.2 + - - +
304C ALA 4.1 1.4 + - - -
305C ILE* 1.3 74.1 - - - +
307C TYR* 1.3 59.8 - - - +
314C ILE* 5.4 0.2 - - - -
315C LEU 3.2 9.6 - - - -
316C GLN* 4.2 5.3 - - - +
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Residues in contact with TYR 307 (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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430B VAL* 4.1 10.4 - - - +
433B PRO* 4.1 16.3 + - + +
281C LEU* 4.1 2.6 - - - +
290C SER 3.3 11.4 - - - +
291C TYR* 3.8 9.6 - - + +
305C ILE 4.1 6.5 - - - -
306C GLY* 1.3 76.2 - - - +
308C VAL* 1.3 73.7 + - - +
309C THR* 3.7 22.4 - - + -
314C ILE* 3.4 7.1 - - - +
315C LEU* 2.8 67.0 + - + +
317C THR* 3.3 22.9 - - - -
336C PHE* 4.1 27.7 - + - +
337C TYR* 3.4 32.1 - + + -
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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
----------------------------------------------------------
281C LEU* 3.8 28.9 - - + +
284C PHE 3.7 17.3 - - - +
285C ILE* 3.7 32.1 - - + +
287C LYS 4.2 8.3 - - - +
288C PRO* 3.9 5.5 - - + +
289C GLY* 3.3 18.3 + - - -
290C SER* 3.0 22.1 + - - +
307C TYR* 1.3 83.0 - - - +
309C THR* 1.3 70.6 + - - +
313C ASN 3.2 9.6 - - - +
314C ILE* 4.6 3.4 - - + -
336C PHE* 4.6 3.1 - - - +
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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