Contacts of the strand formed by residues 332 - 341 (chain C) in PDB entry 5FFO
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 LEU 332 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C PRO* 3.7 32.1 - - + +
330C GLN 4.4 2.9 - - - +
331C ALA* 1.3 82.7 - - - +
333C GLU* 1.3 68.0 + - - +
334C PRO* 4.4 2.3 - - - +
352C ASN* 3.4 50.6 + - + +
353C MET 4.5 2.5 - - - +
354C ILE 3.1 8.5 - - - +
355C VAL* 4.1 21.8 - - + -
16D ARG* 5.5 2.7 - - - +
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Residues in contact with GLU 333 (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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331C ALA* 5.6 0.7 - - + -
332C LEU* 1.3 79.4 - - - +
334C PRO* 1.3 74.4 - - + +
352C ASN* 4.2 1.8 - - - -
353C MET 2.8 7.4 + - - -
354C ILE* 2.7 55.2 + - + +
356C ARG* 2.7 54.4 + - + +
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Residues in contact with PRO 334 (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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332C LEU 4.4 2.9 - - - +
333C GLU* 1.3 93.0 - - + +
335C LEU* 1.3 57.6 + - - +
336C PRO* 4.1 5.5 - - - +
349C GLN* 3.4 26.4 + - + +
350C LEU 3.1 20.0 - - - +
351C SER* 4.2 3.1 - - - -
352C ASN 3.8 11.4 - - - +
353C MET 4.4 0.4 - - - +
354C ILE* 3.5 8.1 - - - +
58D ARG* 4.1 13.2 - - - +
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PHE* 5.0 3.6 - - + -
285C PRO* 4.1 17.7 - - + -
288C TYR* 3.6 51.6 - - + -
334C PRO* 1.3 74.0 - - - +
336C PRO* 1.3 81.6 - - + +
337C ILE* 3.7 16.0 + - + +
349C GLN* 3.8 3.4 - - - -
350C LEU* 2.8 37.2 + - + +
353C MET* 4.1 17.6 - - + +
354C ILE* 3.7 13.7 - - + -
24D ILE* 6.1 1.6 - - + -
52D TYR* 5.1 1.8 - - - +
56D ARG* 6.2 1.1 - - - -
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Residues in contact with PRO 336 (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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285C PRO* 3.4 12.6 - - - +
334C PRO 4.1 5.4 - - - +
335C LEU* 1.3 92.0 - - + +
337C ILE* 1.3 60.7 + - - +
347C VAL* 5.6 3.8 - - + -
348C GLU 3.5 7.4 - - - +
349C GLN* 3.9 17.0 - - + +
52D TYR* 3.1 34.9 + - + -
55D THR* 3.6 32.3 - - + +
56D ARG* 3.7 21.3 - - + +
79D VAL* 6.2 0.4 - - + -
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Residues in contact with ILE 337 (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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273C PHE* 5.4 3.4 - - + -
282C ILE* 4.6 19.1 - - + -
284C GLU 3.3 7.2 - - - +
285C PRO* 4.4 6.1 - - + -
335C LEU* 4.1 24.7 - - + +
336C PRO* 1.3 78.8 - - - +
338C VAL* 1.3 69.3 + - - +
339C TYR* 4.0 24.0 - - + -
347C VAL* 3.5 2.8 - - - +
348C GLU* 2.6 47.1 + - + +
350C LEU* 4.2 22.0 - - + -
24D ILE* 5.0 4.5 - - + -
28D LEU* 4.1 28.0 - - + -
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Residues in contact with VAL 338 (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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282C ILE* 3.7 4.1 - - - +
283C HIS* 3.0 38.6 + - + +
284C GLU* 2.7 25.7 + - + +
337C ILE* 1.3 80.7 - - - +
339C TYR* 1.3 67.8 + - - +
340C TYR* 5.1 8.5 - - + -
345C PRO* 5.5 4.0 - - + -
346C LYS 3.9 4.0 - - - +
347C VAL* 3.8 31.6 - - + -
44D LEU* 5.9 3.4 - - + -
48D VAL* 5.2 12.6 - - + +
49D LEU* 6.6 0.2 - - + -
52D TYR* 4.0 21.3 - - + -
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Residues in contact with TYR 339 (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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281C TRP* 3.7 42.6 - + + +
282C ILE* 4.6 3.4 - - + -
283C HIS* 4.6 0.4 - - - -
337C ILE* 4.0 18.4 - - + -
338C VAL* 1.3 75.2 - - - +
340C TYR* 1.3 73.8 + - - +
341C VAL* 3.5 21.7 - - + +
345C PRO* 3.6 1.6 - - - +
346C LYS* 2.7 47.9 + - + +
348C GLU* 3.0 48.2 + - + -
28D LEU* 4.0 22.6 + - + +
30D LEU* 5.1 8.8 - - + +
34D PRO* 4.9 2.2 - - + -
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Residues in contact with TYR 340 (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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281C TRP* 4.4 4.8 + - - +
283C HIS* 3.3 40.6 - + + -
338C VAL* 5.1 6.3 - - + -
339C TYR* 1.3 92.2 - - - +
341C VAL* 1.3 62.9 + - - +
342C GLY 4.0 1.2 + - - -
343C ARG 4.4 9.6 - - - -
344C LYS 3.5 4.5 - - - -
345C PRO* 3.4 41.6 - - + +
34D PRO* 3.9 16.3 - - - +
35D SER 5.5 0.5 - - - +
36D GLN* 6.2 0.2 - - + -
39D VAL* 3.5 39.6 - - + +
40D PRO* 4.6 13.2 - - + +
43D PRO 3.6 20.1 + - - -
44D LEU* 3.7 9.7 - - + +
45D PRO* 4.3 10.6 - - - +
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Residues in contact with VAL 341 (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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339C TYR* 3.5 25.4 - - + +
340C TYR* 1.3 78.6 - - - +
342C GLY* 1.3 59.3 + - - +
343C ARG 2.8 10.2 + - - -
344C LYS* 2.6 34.0 + - + +
346C LYS* 3.5 34.1 - - + -
34D PRO* 5.4 5.8 - - + -
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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