Contacts of the strand formed by residues 357 - 361 (chain C) in PDB entry 5HVO
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 ILE 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C LEU* 4.0 26.0 - - + -
301C LEU* 3.5 18.8 - - + -
317C LEU* 3.5 11.4 - - + +
319C GLN* 5.0 3.8 - - + -
342C VAL* 4.3 21.1 - - + +
345C ILE* 3.6 38.1 - - + -
346C ASN* 2.9 33.0 + - - +
355C MET* 4.1 3.6 - - - +
356C PRO* 1.3 82.3 - - + +
358C HIS* 1.3 68.3 + - - +
359C PHE* 3.7 23.3 + - + +
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Residues in contact with HIS 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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276C PHE* 4.2 22.8 - + - -
316C VAL* 3.4 26.2 - - + +
317C LEU 2.7 13.1 + - - +
318C VAL* 3.3 18.8 - - + +
319C GLN 2.7 31.6 + - - +
354C TYR* 5.9 0.2 - + - -
355C MET* 3.2 31.1 + - + -
357C ILE* 1.3 76.8 + - - +
359C PHE* 1.3 56.8 + - - +
360C MET* 3.9 7.4 + - + +
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Residues in contact with PHE 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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288C LEU* 4.7 6.3 - - + -
294C ILE* 6.0 0.2 - - + -
319C GLN* 3.5 21.3 - - + -
321C ALA* 3.4 29.2 - - + -
335C ARG* 6.2 0.2 - - - -
338C VAL* 4.0 21.5 - - + -
339C ASN* 3.5 26.5 - - - -
342C VAL* 3.9 38.6 - - + -
357C ILE* 3.7 10.9 + - + -
358C HIS* 1.3 72.0 - - - +
360C MET* 1.3 63.9 + - - +
361C HIS* 4.2 21.4 + + + -
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Residues in contact with MET 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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318C VAL* 3.4 33.0 - - + -
319C GLN 2.9 11.4 + - - +
320C VAL* 3.7 21.3 - - + +
321C ALA* 2.8 28.6 + - - -
358C HIS* 4.5 6.5 - - + +
359C PHE* 1.3 79.4 - - - +
361C HIS* 1.3 60.3 + - - +
362C LYS* 3.2 38.8 + - + +
364C VAL* 5.9 2.0 - - + -
368C GLU* 6.1 0.2 - - - +
372C LEU* 4.7 10.1 - - + -
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Residues in contact with HIS 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LEU* 3.6 28.5 - - + +
321C ALA* 3.3 18.6 - - + -
323C PRO* 3.7 28.6 - - + +
324C SER 5.1 0.2 + - - -
326C GLN* 3.8 19.3 + - - -
335C ARG* 3.4 40.2 + - - +
359C PHE* 4.2 19.0 + + + -
360C MET* 1.3 67.6 - - - +
362C LYS* 1.3 63.9 + - - +
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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