Contacts of the strand formed by residues 311 - 316 (chain C) in PDB entry 3MSS
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 PHE 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C THR* 3.1 28.9 + - - -
273C LEU* 3.3 20.9 + - + -
280C VAL* 3.6 30.3 - - + -
283C PHE* 3.5 25.7 - + + -
284C LEU* 3.7 28.3 - - + -
305C CYS 3.1 11.2 - - - +
306C THR* 3.8 21.1 - - + -
307C ARG 3.9 5.4 - - - -
308C GLU* 3.0 35.0 - - - -
309C PRO* 3.5 12.7 - - + +
310C PRO* 1.3 69.9 - - - +
312C TYR* 1.3 57.3 + - - +
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Residues in contact with TYR 312 (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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239C ARG* 3.7 36.4 + - + +
242C ILE* 4.9 5.2 - - + -
244C MET* 3.6 41.4 - - + +
270C VAL* 3.5 21.8 - - + -
271C LYS 3.2 2.5 - - - -
272C THR* 3.7 15.0 - - - -
283C PHE* 3.8 1.1 - - - -
304C VAL* 3.4 5.5 - - - +
305C CYS* 2.9 55.3 + - + +
306C THR* 4.0 2.9 - - - +
310C PRO* 3.5 19.3 + - + +
311C PHE* 1.3 81.6 - - - +
313C ILE* 1.3 65.5 + - - +
314C ILE* 4.2 12.3 - - + -
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Residues in contact with ILE 313 (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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1C STI 3.6 30.6 - - + +
270C VAL* 3.4 2.1 - - - -
271C LYS* 2.7 38.5 + - + -
283C PHE* 3.6 37.7 - - + +
286C GLU* 4.2 18.2 - - + +
287C ALA* 3.7 36.3 - - + +
290C MET* 3.9 6.3 - - + -
301C LEU* 3.8 21.8 - - + -
303C GLY 3.9 3.6 - - - -
304C VAL* 4.4 2.9 - - + -
312C TYR* 1.3 74.6 - - - +
314C ILE* 1.3 63.8 + - - +
315C THR* 4.6 0.4 - - + -
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Residues in contact with ILE 314 (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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237C MET* 3.3 26.2 - - + -
242C ILE* 2.8 38.8 - - + -
261C TRP* 5.1 2.5 - - + -
268C VAL* 3.8 34.8 - - + -
269C ALA 3.3 3.8 - - - +
270C VAL* 4.2 8.5 - - + -
301C LEU* 3.5 6.2 - - - +
302C LEU* 2.8 33.3 + - + -
303C GLY 2.8 22.6 + - - +
305C CYS* 4.5 2.9 - - - -
312C TYR* 4.2 20.2 - - + -
313C ILE* 1.3 77.9 - - - +
315C THR* 1.3 64.4 + - - +
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Residues in contact with THR 315 (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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1C STI 3.0 50.9 + - + -
268C VAL* 3.5 6.9 - - - +
269C ALA* 2.8 36.2 + - - +
290C MET* 3.9 18.8 - - + -
299C VAL* 4.0 9.4 - - + +
300C GLN 3.3 17.3 - - - +
301C LEU* 4.3 0.4 - - - -
302C LEU* 3.5 7.4 - - - -
313C ILE* 4.6 0.9 - - + -
314C ILE* 1.3 78.1 - - - +
316C GLU* 1.3 71.0 + - - +
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Residues in contact with GLU 316 (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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1C STI 4.2 4.5 - - - -
266C LEU* 6.1 1.8 - - + -
267C THR 5.0 1.1 - - - -
268C VAL* 4.9 0.9 - - - +
269C ALA* 4.0 4.2 - - - +
299C VAL* 3.5 10.7 - - + +
300C GLN* 2.7 47.8 + - + +
302C LEU* 3.4 16.3 - - + +
315C THR* 1.3 88.3 + - - +
317C PHE* 1.3 60.5 + - - +
318C MET* 3.8 15.6 + - - +
376C LEU* 5.6 0.5 - - - +
378C LYS* 2.6 46.9 + - - +
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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