Contacts of the strand formed by residues 280 - 287 (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 LYS 280 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C GLY 4.2 1.0 + - - -
279C THR* 1.3 71.6 - - - +
281C LEU* 1.3 59.6 + - - +
282C MET* 5.9 0.7 - - + -
311C TRP* 3.8 30.8 - - + -
314C LYS 2.9 8.6 + - - +
315C VAL* 3.4 7.5 - - + +
316C VAL 3.0 25.3 + - - -
377C ASP* 3.8 27.8 - - + -
440C VAL* 3.0 46.9 + - + +
447C ARG* 4.2 19.5 - - - +
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 5.2 3.6 - - + +
276C PHE* 4.3 36.8 - - + -
279C THR 3.4 5.5 + - - +
280C LYS* 1.3 73.9 - - - +
282C MET* 1.3 64.0 + - - +
316C VAL* 4.0 13.9 - - + +
318C VAL* 3.5 29.6 - - + -
372C LEU* 4.9 10.1 - - + -
375C ALA* 3.8 31.6 - - + +
376C SER* 3.7 16.1 - - - +
377C ASP* 2.9 39.1 + - - +
378C ALA 3.3 5.5 + - - -
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Residues in contact with MET 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LYS* 5.9 0.4 - - + -
281C LEU* 1.3 75.9 - - - +
283C VAL* 1.3 56.1 + - - +
301C LEU* 5.3 7.4 - - - -
304C PHE* 6.0 0.4 - - - -
315C VAL* 4.2 20.6 - - + -
316C VAL 2.7 17.1 + - - +
317C LEU* 3.3 15.4 - - + +
318C VAL* 2.6 35.3 + - - +
376C SER* 4.3 0.9 - - - -
377C ASP* 6.2 0.2 - - + -
378C ALA* 3.3 24.7 - - + +
380C VAL* 3.1 35.2 - - + -
407C ILE* 4.0 10.5 - - + -
436C TYR* 3.4 35.9 - - + +
439C ALA* 5.4 0.2 - - + -
440C VAL* 4.6 13.2 - - + -
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C MET* 1.3 76.2 - - - +
284C SER* 1.3 73.4 + - - +
285C VAL* 4.1 12.8 - - + -
317C LEU* 4.2 1.3 - - - -
318C VAL* 3.3 11.2 - - + +
320C VAL* 5.2 0.9 - - + -
372C LEU* 4.4 26.5 - - + +
373C TYR* 4.5 8.3 - - + -
376C SER* 3.1 32.7 + - - +
378C ALA 2.8 14.2 + - - +
379C CYS* 3.1 21.5 - - + -
380C VAL 2.9 24.8 + - - -
395C TYR* 4.2 9.0 - - + -
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL* 1.3 74.5 + - - +
285C VAL* 1.3 62.1 + - - +
286C ASP* 3.6 1.3 - - - -
297C LYS* 3.0 23.1 + - - +
317C LEU* 3.9 4.7 - - - +
318C VAL 2.9 9.4 + - - +
319C GLN* 3.1 28.0 - - - -
320C VAL* 2.8 31.4 + - - +
379C CYS* 5.0 2.2 - - - -
380C VAL* 2.9 28.1 + - - +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL* 4.1 11.0 - - + -
284C SER* 1.3 78.3 - - - +
286C ASP* 1.3 70.0 + - - +
320C VAL* 3.6 20.4 - - + -
322C VAL* 4.4 4.0 - - + -
369C LEU* 3.9 13.0 - - + -
372C LEU* 6.1 1.6 - - + -
373C TYR* 3.8 34.8 - - + +
379C CYS* 5.5 0.4 - - - -
380C VAL 5.2 0.6 + - - -
389C ASN* 5.8 0.2 + - - -
391C VAL* 3.4 32.3 - - + +
501C UDP 3.6 37.7 - - + -
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Residues in contact with ASP 286 (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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284C SER* 3.6 0.7 - - - -
285C VAL* 1.3 85.4 + - - +
287C ARG* 1.3 71.2 + - - +
292C LYS* 3.6 40.9 - - + +
294C ILE* 4.8 3.8 - - + -
297C LYS* 3.2 19.4 + - - -
319C GLN* 3.2 18.0 + - - +
320C VAL 2.9 10.4 + - - +
321C ALA* 3.3 2.9 - - - -
322C VAL* 2.8 23.6 + - - +
380C VAL 4.7 2.5 - - - +
381C VAL* 5.1 7.8 - - - +
383C SER* 4.9 1.4 + - - -
389C ASN* 4.7 8.3 + - - -
391C VAL* 5.6 0.2 - - - -
501C UDP 6.5 0.9 - - - -
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Residues in contact with ARG 287 (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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105C TRP* 3.4 29.1 - - - -
286C ASP* 1.3 85.9 - - - +
288C LEU* 1.3 59.8 + - - +
289C ASP* 2.8 36.0 + - + +
292C LYS* 3.7 18.0 - - - +
294C ILE* 4.4 1.4 - - - +
322C VAL* 3.0 34.8 - - + +
323C PRO 5.7 0.2 - - - -
324C SER* 3.2 27.5 + - - -
325C ARG* 4.4 7.5 - - - +
501C UDP 2.6 46.9 + - - +
502C VDM 3.7 23.6 + - - +
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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