Contacts of the strand formed by residues 346 - 351 (chain P) in PDB entry 1SVC
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 LYS 346 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253P ILE* 3.4 45.8 - - + +
254P VAL 4.7 8.4 + - - -
255P ARG* 5.6 2.2 - - - +
256P MET* 4.2 21.3 - - + -
331P PHE* 3.3 8.1 - - - -
332P VAL* 2.7 39.0 + - + +
344P GLU* 4.6 5.2 - - + +
345P PRO* 1.3 83.2 - - - +
347P PRO* 1.3 74.2 - - + +
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Residues in contact with PRO 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P MET* 3.9 14.2 - - - +
259P THR* 4.2 9.5 - - - +
330P VAL 4.0 5.4 - - - +
331P PHE* 4.3 12.8 - - + -
345P PRO 4.4 2.5 - - - +
346P LYS* 1.3 100.1 - - + +
348P PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P MET* 4.5 3.4 - - + -
258P ARG 4.1 3.1 - - - -
259P THR* 3.4 18.4 - - - -
260P ALA 3.5 18.6 - - - -
261P GLY* 3.4 27.4 - - - -
269P ILE* 4.0 18.8 - - + -
285P PHE* 3.7 22.9 - + - -
316P THR* 3.9 17.7 - - + -
329P SER* 3.5 3.7 - - - -
330P VAL* 2.9 56.3 + - + +
332P VAL* 3.7 19.5 - - + -
347P PRO* 1.3 76.2 - - - +
349P LEU* 1.3 59.9 + - - +
350P TYR* 3.8 26.9 - + - -
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Residues in contact with LEU 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259P THR 3.0 10.2 + - - +
260P ALA* 3.2 34.1 - - + +
261P GLY 3.3 3.6 + - - -
327P PRO* 3.7 37.2 - - + +
328P ALA 3.7 10.1 - - - +
329P SER* 3.3 24.2 - - - +
348P PHE* 1.3 73.6 - - - +
350P TYR* 1.3 61.4 + - - +
351P TYR* 3.7 7.8 + - + -
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Residues in contact with TYR 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P GLY 3.5 9.4 - - - +
262P CYS 3.9 11.7 - - - -
263P VAL* 3.6 30.2 - - + +
265P GLY* 5.3 0.7 - - - -
285P PHE* 4.1 3.7 - + - -
295P TRP* 3.8 10.4 - + - -
316P THR* 5.5 2.0 - - - -
317P PRO* 2.9 42.8 + - - +
319P TYR* 3.6 38.5 + + + -
327P PRO* 3.3 6.8 - - - +
328P ALA* 2.9 39.4 + - + +
330P VAL* 3.4 35.4 - - + -
348P PHE* 3.8 18.6 - + - -
349P LEU* 1.3 71.9 - - - +
351P TYR* 1.3 59.1 + - - +
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Residues in contact with TYR 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260P ALA* 3.9 23.8 + - + -
261P GLY* 3.2 16.0 + - - -
262P CYS* 3.5 26.7 + - + +
263P VAL* 2.9 30.4 + - - +
267P GLU* 5.6 2.8 - - - +
327P PRO* 4.4 8.3 - - + -
349P LEU* 4.3 13.0 - - + -
350P TYR* 1.3 73.6 - - - +
352P PRO* 1.4 72.8 - - + +
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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