Contacts of the strand formed by residues 373 - 380 (chain C) in PDB entry 5FLZ
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 SER 373 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C PHE* 5.9 1.6 - - - -
273C THR* 3.6 15.0 - - - -
274C PRO* 3.5 16.9 - - - +
292C TYR* 4.3 9.7 - - - -
323C ILE* 3.8 8.3 - - - +
324C GLY* 2.9 28.6 + - - +
362C TYR* 3.1 24.2 + - - -
371C GLU* 3.3 7.3 + - - +
372C VAL* 1.4 75.2 + - - +
374C GLY* 1.4 61.6 + - - +
375C MET* 6.1 1.6 - - - -
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Residues in contact with GLY 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PHE* 3.7 3.4 - - - -
273C THR 2.9 31.8 + - - +
292C TYR* 3.3 20.7 - - - -
322C ILE 3.1 14.4 - - - -
324C GLY 4.3 1.8 - - - -
373C SER* 1.4 80.0 - - - +
375C MET* 1.4 66.6 + - - -
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Residues in contact with MET 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ILE* 5.9 0.9 - - + -
237C SER* 3.6 31.4 - - - +
238C VAL* 4.0 26.0 - - + +
240C ASN* 5.4 2.2 - - + -
241C SER* 5.7 1.1 - - - +
270C PRO* 6.1 1.6 - - + -
271C SER 3.4 7.6 - - - +
272C PHE* 3.8 25.4 - - + -
292C TYR* 3.0 6.0 + - - -
322C ILE* 2.8 76.3 + - + +
324C GLY* 5.7 4.9 - - - +
358C ARG* 4.6 4.5 - - - +
360C SER* 4.0 12.1 - - - +
373C SER* 6.1 1.3 - - - -
374C GLY* 1.4 77.1 - - - -
376C MET* 1.3 56.4 + - - +
377C LEU* 5.5 2.7 - - + -
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Residues in contact with MET 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C SER 3.8 4.9 - - - +
270C PRO* 3.2 9.2 - - - +
271C SER* 3.0 59.0 + - - +
292C TYR* 3.3 2.0 + - - +
296C LEU* 3.8 30.3 - - + +
297C ASP* 6.0 1.3 - - - +
312C ASN* 5.8 1.6 - - - +
316C PHE* 5.6 2.9 - - + -
319C TYR* 3.4 25.8 - - + -
320C ASN 3.3 15.7 - - - +
321C THR* 4.3 3.1 - - - +
375C MET* 1.3 73.8 - - - +
377C LEU* 1.4 68.5 + - - +
378C SER* 3.4 30.1 - - - +
380C MET* 5.1 12.8 - - + -
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C VAL* 5.4 10.1 - - + -
238C VAL* 4.9 26.7 - - + -
255C ILE* 4.7 14.6 - - + -
259C LEU* 3.9 26.2 - - + +
268C LEU* 5.1 9.0 - - + -
269C SER 3.8 3.4 - - - +
270C PRO* 4.3 15.9 - - + -
319C TYR 3.9 0.5 - - - -
320C ASN* 2.9 39.9 + - + +
322C ILE* 4.5 22.6 - - + +
358C ARG* 5.4 0.9 - - - +
375C MET* 4.5 2.6 + - + -
376C MET* 1.4 79.7 - - - +
378C SER* 1.4 60.1 + - - +
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Residues in contact with SER 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU* 3.5 10.5 - - - +
269C SER* 2.9 37.7 + - - +
316C PHE* 5.0 2.4 - - - -
318C VAL* 3.5 12.6 - - - -
319C TYR* 3.5 16.5 - - - -
376C MET* 3.4 36.4 - - - +
377C LEU* 1.4 73.2 + - - +
379C ASN* 1.3 58.8 + - - +
380C MET* 3.9 18.6 - - - -
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Residues in contact with ASN 379 (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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259C LEU 4.5 5.9 + - - -
260C ILE* 5.1 1.4 - - - +
265C LEU* 3.6 27.5 - - - +
266C HIS* 3.6 24.7 + - - +
267C PHE* 3.2 23.8 + - - +
268C LEU* 4.0 10.0 - - + +
316C PHE* 3.9 0.2 - - - -
317C ASN* 2.9 38.8 + - - +
318C VAL* 3.2 29.7 + - + +
378C SER* 1.3 70.1 - - - +
380C MET* 1.4 66.0 + - - +
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Residues in contact with MET 380 (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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265C LEU* 6.4 0.9 - - - -
267C PHE* 4.4 5.1 + - - +
269C SER* 3.7 32.0 + - - +
271C SER* 5.8 1.6 - - - +
304C SER* 5.4 1.8 - - - +
306C VAL* 5.2 3.8 - - + -
312C ASN* 3.8 31.6 - - - +
314C THR* 4.7 1.1 - - - +
315C TYR 3.9 7.9 - - - +
316C PHE* 3.3 40.4 - - + -
317C ASN 4.8 0.2 - - - +
376C MET* 5.1 8.5 - - + -
378C SER* 3.9 18.4 + - - -
379C ASN* 1.4 81.5 + - - +
381C SER* 1.4 64.6 + - - +
382C THR* 3.2 17.0 + - + +
383C VAL* 3.7 20.4 + - - +
434C MET* 4.8 1.3 - - - +
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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
------------------------------------------------------------
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