Contacts of the strand formed by residues 344 - 355 (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 LYS 344 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340C TYR* 3.5 1.5 - - - -
341C VAL* 2.6 48.3 + - + +
342C GLY 3.7 0.4 - - - -
343C ARG* 1.3 84.1 - - + +
345C PRO* 1.3 65.5 - - + +
346C LYS* 3.6 19.6 + - - +
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Residues in contact with PRO 345 (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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338C VAL* 5.5 5.2 - - + -
339C TYR 3.6 7.0 - - - +
340C TYR* 3.4 40.1 - - + +
343C ARG 3.5 9.2 - - - +
344C LYS* 1.3 85.4 - - + +
346C LYS* 1.3 62.5 + - - +
347C VAL* 4.2 3.5 + - + +
45D PRO* 5.8 4.0 - - + -
48D VAL* 5.1 17.7 - - + -
78D GLU* 5.5 0.3 - - - +
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Residues in contact with LYS 346 (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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338C VAL* 4.8 1.1 - - - +
339C TYR* 2.7 46.5 + - + +
341C VAL* 3.5 36.1 - - + -
344C LYS* 4.0 18.7 - - + +
345C PRO* 1.3 76.3 - - - +
347C VAL* 1.3 63.4 + - - +
348C GLU* 3.6 30.0 + - + +
78D GLU* 3.9 31.1 + - - +
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Residues in contact with VAL 347 (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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336C PRO* 5.6 3.1 - - + -
337C ILE 3.5 11.9 - - - +
338C VAL* 3.8 25.4 - - + -
345C PRO* 4.2 3.3 + - + +
346C LYS* 1.3 71.3 - - - +
348C GLU* 1.3 56.6 + - - +
48D VAL* 4.1 28.3 - - + +
51D LEU* 4.4 22.9 - - + -
52D TYR* 4.7 13.2 - - + +
55D THR* 5.9 1.3 - - + -
78D GLU* 3.6 3.7 - - - +
79D VAL* 2.7 53.7 + - + +
80D THR* 6.2 0.4 - - - +
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Residues in contact with GLU 348 (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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336C PRO* 3.5 2.4 - - - +
337C ILE* 2.6 47.9 + - + +
339C TYR* 3.0 39.8 + - + -
346C LYS* 3.6 19.4 + - + +
347C VAL* 1.3 79.2 - - - +
349C GLN* 1.3 56.5 + - - +
28D LEU* 3.2 17.8 - - - +
76D ALA* 3.4 14.6 - - + +
77D LYS 3.3 9.0 - - - +
78D GLU* 3.6 27.1 - - + +
79D VAL* 4.5 1.8 - - - -
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Residues in contact with GLN 349 (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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334C PRO* 3.4 32.8 + - + +
335C LEU 3.5 15.3 - - - +
336C PRO* 3.9 15.5 - - + +
348C GLU* 1.3 74.3 - - - +
350C LEU* 1.3 71.4 + - - +
351C SER* 3.9 1.4 + - - -
55D THR* 5.0 14.3 + - - +
58D ARG* 3.5 17.9 + - - +
75D TYR 5.0 0.3 - - - +
76D ALA* 4.1 1.3 - - - -
77D LYS* 3.0 31.6 + - + +
79D VAL* 3.8 21.6 - - + +
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Residues in contact with LEU 350 (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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334C PRO* 3.1 9.1 - - - +
335C LEU* 2.8 37.9 + - + +
337C ILE* 4.2 22.0 - - + -
349C GLN* 1.3 73.8 - - - +
351C SER* 1.3 60.3 + - - +
353C MET* 3.8 29.4 - - + -
24D ILE* 3.8 38.8 - - + +
27D LYS* 3.8 21.1 - - + -
28D LEU* 4.1 13.7 - - + -
76D ALA* 3.7 27.1 - - + +
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Residues in contact with SER 351 (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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334C PRO* 4.2 5.6 - - - -
349C GLN 3.9 2.1 + - - -
350C LEU* 1.3 72.4 - - - +
352C ASN* 1.3 73.8 + - - +
27D LYS* 2.4 35.3 + - - +
73D ASP* 3.1 28.7 + - - -
74D TYR* 3.3 17.8 + - - -
75D TYR 4.0 5.9 + - - -
77D LYS* 6.4 0.9 - - - -
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Residues in contact with ASN 352 (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* 3.4 47.6 + - + +
333C GLU 3.9 5.8 - - - -
334C PRO* 3.8 11.5 - - - +
351C SER* 1.3 89.7 + - - +
353C MET* 1.3 59.7 + - - +
23D GLN* 3.8 7.4 + - - -
27D LYS* 3.3 9.0 + - - -
73D ASP* 5.7 1.0 + - - -
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Residues in contact with MET 353 (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 31.6 - - + +
290C ALA* 3.7 5.7 - - - +
332C LEU* 4.9 2.6 - - - +
333C GLU 2.8 9.1 + - - +
335C LEU* 4.1 21.1 - - + -
350C LEU* 3.8 33.4 - - + +
351C SER 4.4 0.4 - - - +
352C ASN* 1.3 74.8 - - - +
354C ILE* 1.3 68.3 + - + +
355C VAL* 3.4 1.2 + - - +
16D ARG* 3.0 28.1 + - - +
20D ILE* 3.7 9.9 - - + -
23D GLN* 3.3 26.0 - - - +
24D ILE* 4.1 20.2 - - + -
27D LYS* 3.3 26.9 - - - +
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Residues in contact with ILE 354 (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* 3.9 16.4 - - + -
289C HIS* 3.3 26.5 - - + +
290C ALA* 3.8 3.8 - - - +
291C ASN* 5.4 2.0 - - - +
332C LEU* 3.1 6.0 - - - -
333C GLU* 2.7 71.4 + - + +
334C PRO 3.5 16.6 - - - +
335C LEU* 3.7 23.1 - - + -
353C MET* 1.3 69.0 - - - +
355C VAL* 1.3 69.7 + - - +
356C ARG* 3.5 9.7 + - - +
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Residues in contact with VAL 355 (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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253C THR* 4.8 1.0 - - - +
266C VAL* 3.9 8.3 - - + +
290C ALA 2.8 20.8 + - - +
291C ASN* 3.6 29.2 + - - +
292C PHE* 4.6 4.0 - - - -
293C CYS* 3.7 18.2 - - - -
329C PRO* 3.7 27.6 - - + -
331C ALA 4.0 2.7 - - - -
332C LEU* 4.1 17.3 - - + -
354C ILE* 1.3 75.5 - - - +
356C ARG* 1.3 62.4 + - - +
357C SER 3.7 5.6 - - - +
358C CYS* 4.1 3.6 - - - -
16D ARG* 3.8 27.4 - - - +
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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