Contacts of the strand formed by residues 355 - 360 (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 ASN 355 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638A HIS* 3.0 21.0 + - - -
642A THR* 5.0 2.3 + - - +
645A GLU* 4.6 2.8 - - - +
316C PHE* 5.7 2.6 - - - -
319C TYR* 3.6 35.0 - - + +
336C THR* 5.8 8.1 - - + -
340C GLN* 3.7 31.0 + - + +
347C TRP* 5.8 2.8 - - - +
353C HIS* 3.8 17.3 + - - +
354C VAL* 1.4 81.1 + - - +
356C ILE* 1.4 60.1 + - - +
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Residues in contact with ILE 356 (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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638A HIS* 3.5 22.0 - - + +
641A LYS* 3.6 34.1 - - + -
645A GLU* 3.7 4.9 - - - +
258C THR* 2.8 53.2 - - + +
259C LEU* 4.2 12.6 - - + -
318C VAL* 6.0 1.8 - - + -
319C TYR* 3.0 17.2 + - - +
320C ASN* 3.4 17.7 - - + +
321C THR* 3.0 24.1 + - - +
354C VAL 5.3 0.7 - - - -
355C ASN* 1.4 75.5 - - - +
357C GLY* 1.4 65.8 + - - +
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Residues in contact with GLY 357 (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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641A LYS* 3.5 8.7 + - - -
645A GLU* 3.0 33.2 + - - +
320C ASN* 3.8 2.2 - - - -
321C THR* 3.3 16.4 - - - -
356C ILE* 1.4 78.2 - - - +
358C ARG* 1.4 60.0 + - - -
359C ARG* 3.6 4.9 + - - -
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Residues in contact with ARG 358 (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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641A LYS* 5.2 6.1 - - - +
238C VAL* 3.6 19.0 + - - +
241C SER* 3.3 22.7 + - - -
242C ILE* 5.2 1.2 - - - +
247C TYR* 5.2 2.5 - - + -
249C TYR 4.2 7.9 - - - -
250C SER* 3.1 28.3 + - - +
255C ILE* 2.5 41.4 - - - +
320C ASN* 3.7 7.6 + - - +
321C THR 2.8 6.6 + - - +
322C ILE* 2.5 56.0 - - + +
323C ILE* 2.8 28.1 + - - +
357C GLY* 1.4 59.4 - - - +
359C ARG* 1.4 87.1 + - - +
360C SER* 5.0 0.4 - - - -
375C MET* 4.6 3.2 - - - +
377C LEU* 5.4 1.4 - - - +
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Residues in contact with ARG 359 (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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641A LYS* 4.1 6.1 - - - +
645A GLU* 3.7 19.4 + - - +
648A ASN* 3.6 37.5 + - - +
649A GLN* 4.5 17.1 - - + +
653A ASP* 4.1 12.1 - - - +
247C TYR* 3.0 51.5 + - - +
249C TYR* 4.0 25.1 - - - +
323C ILE* 3.4 11.7 - - + +
325C ASN 5.8 2.2 - - - +
329C ARG* 6.6 0.4 - - + -
357C GLY 3.6 21.4 + - - -
358C ARG* 1.4 90.0 - - - +
360C SER* 1.4 63.6 + - - +
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Residues in contact with SER 360 (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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240C ASN* 4.9 2.5 + - - +
241C SER* 3.9 28.5 - - - -
247C TYR* 4.1 2.9 - - - -
322C ILE* 3.8 16.5 - - - +
323C ILE 2.8 23.0 + - - +
324C GLY* 3.5 11.6 - - - -
325C ASN 3.5 8.1 + - - +
358C ARG* 5.0 1.1 - - - -
359C ARG* 1.4 75.4 - - - +
361C PRO* 1.4 74.2 + - - +
375C MET* 4.0 11.2 - - - +
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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