Contacts of the strand formed by residues 316 - 326 (chain C) in PDB entry 5O67
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 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C TYR* 3.3 7.8 - - - +
289C THR* 3.0 40.7 + - - +
291C ASN* 5.7 0.5 + - - -
315C ASP* 1.3 80.5 - - - +
317C PHE* 1.3 61.3 + - - +
318C GLN* 2.6 23.7 + - - -
340C LEU* 4.4 6.7 - - - +
341C ILE 3.2 14.1 - - - -
342C GLN* 3.9 17.0 - - - -
343C ARG* 5.8 0.7 - - - -
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Residues in contact with PHE 317 (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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286C VAL* 3.9 26.2 - - + -
287C SER 3.6 11.4 - - - -
288C TYR* 4.6 11.0 - + + -
316C SER* 1.3 73.7 - - - +
318C GLN* 1.3 59.5 + - - +
319C PHE* 3.6 32.4 - + + -
339C ASP 4.2 0.7 - - - +
340C LEU* 3.7 0.9 - - - -
341C ILE* 2.9 46.5 + - + +
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Residues in contact with GLN 318 (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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268C THR* 4.5 3.6 - - - +
286C VAL* 3.5 3.6 - - - +
287C SER* 2.8 70.5 + - - +
288C TYR* 4.0 1.2 - - - +
289C THR* 3.7 16.5 + - - -
316C SER* 2.6 37.2 + - - +
317C PHE* 1.3 73.3 - - - +
319C PHE* 1.3 64.0 + - - +
339C ASP 3.5 7.4 - - - +
340C LEU* 3.7 28.3 - - + +
501C LDA 3.7 24.0 - - + -
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Residues in contact with PHE 319 (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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285C SER 3.5 13.0 - - - +
286C VAL* 4.0 13.9 - - + +
317C PHE* 3.6 27.8 - + + -
318C GLN* 1.3 75.6 - - - +
320C GLY* 1.3 65.7 + - - +
321C VAL* 6.1 1.1 - - + -
338C SER* 3.2 6.0 - - - -
339C ASP* 2.9 60.8 + - + +
341C ILE* 4.4 14.8 - - + -
501C LDA 5.0 5.8 - - - -
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 6.2 0.2 - - - -
284C GLY* 3.6 1.0 - - - -
285C SER* 3.1 37.2 + - - +
319C PHE* 1.3 83.4 - - - +
321C VAL* 1.3 63.5 + - - +
337C VAL 3.1 14.1 - - - -
338C SER* 3.6 8.1 - - - -
501C LDA 5.3 0.8 - - - +
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Residues in contact with VAL 321 (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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398A PHE* 4.5 13.2 - - + -
283C PHE* 3.6 18.4 - - - +
284C GLY* 4.1 3.4 - - - -
319C PHE* 6.1 1.3 - - + -
320C GLY* 1.3 75.4 - - - +
322C GLY* 1.3 61.6 + - - +
336C SER* 3.3 5.1 - - - -
337C VAL* 2.8 46.3 + - + +
505C C8E 4.0 51.1 - - + -
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Residues in contact with GLY 322 (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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282C LEU* 3.8 6.9 - - - +
283C PHE* 2.9 46.4 + - - +
321C VAL* 1.3 80.1 - - - +
323C VAL* 1.3 62.1 + - - +
335C PHE 3.4 11.4 - - - -
336C SER* 3.8 1.8 - - - -
505C C8E 4.6 11.4 - - - +
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Residues in contact with VAL 323 (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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333A MET* 4.1 27.8 - - + -
371A MET* 4.5 16.2 - - + -
280C ALA* 4.4 10.1 - - + -
281C VAL 3.4 11.2 - - - +
282C LEU* 4.1 18.4 - - + -
283C PHE* 3.6 4.3 - - - -
322C GLY* 1.3 76.1 - - - +
324C ALA* 1.3 66.5 + - - +
325C PHE* 3.9 24.2 - - + -
334C SER* 3.7 0.2 - - - -
335C PHE* 2.8 44.6 + - + +
505C C8E 4.9 8.5 - - + -
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Residues in contact with ALA 324 (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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95C LEU* 4.0 25.4 - - + -
281C VAL* 2.8 40.2 + - - +
283C PHE* 3.9 16.4 - - + -
323C VAL* 1.3 77.0 - - - +
325C PHE* 1.3 68.4 + - - +
332C SER* 5.8 0.4 - - - +
333C MET 3.3 13.2 - - - +
334C SER* 4.2 8.3 - - - +
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Residues in contact with PHE 325 (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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327A LEU* 3.6 28.5 - - + -
333A MET* 3.8 29.8 - - - -
95C LEU* 4.1 5.8 - - - -
279C PRO* 3.8 23.8 - - + +
280C ALA* 4.0 18.4 - - + -
281C VAL* 5.4 0.2 - - - -
323C VAL* 3.9 14.6 - - + -
324C ALA* 1.3 80.3 - - - +
326C ALA* 1.3 65.6 + - - +
327C LEU* 3.5 10.5 + - + +
332C SER* 3.3 2.1 - - - -
333C MET* 2.9 41.5 + - + -
335C PHE* 4.2 22.0 - + - -
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Residues in contact with ALA 326 (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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91C SER* 3.2 21.8 - - - +
92C VAL* 4.5 17.5 - - + -
95C LEU* 4.0 10.7 - - + +
279C PRO* 4.7 6.6 + - - +
281C VAL* 5.8 0.4 - - - +
325C PHE* 1.3 72.8 - - - +
327C LEU* 1.3 63.2 + - - +
328C ASN 3.4 3.1 - - - +
331C MET 3.8 5.2 - - - -
332C SER* 4.3 2.0 - - - +
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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