Contacts of the helix formed by residues 313 - 329 (chain C) in PDB entry 6NYY
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 CYS 313 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C VAL* 3.7 28.3 - - - -
311C ALA 2.9 11.7 + - - -
312C GLY* 1.3 67.1 - - - -
314C GLU* 1.3 63.1 + - - +
315C GLU 3.6 1.3 - - - -
316C ALA* 3.9 13.0 - - + -
317C LYS* 3.3 21.7 + - - +
352C THR 4.8 0.9 - - - +
353C GLY 4.6 4.7 - - - -
357C LEU* 4.6 14.6 - - - -
475C ILE* 3.9 30.7 - - + -
476C GLY 5.6 2.5 - - - +
478C PRO* 5.2 0.8 - - - +
803C ANP 4.5 5.8 + - - -
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Residues in contact with GLU 314 (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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560B THR* 4.1 12.3 - - + +
310C VAL 5.5 0.5 - - - +
311C ALA* 5.7 1.0 - - - -
312C GLY 2.9 8.8 + - - +
313C CYS* 1.3 71.5 - - - +
315C GLU* 1.3 76.2 + - + +
316C ALA 3.2 0.2 - - - -
317C LYS* 3.3 35.7 + - - +
318C LEU* 3.4 9.7 + - - +
768C GLU* 3.3 19.0 - - - +
769C ASP 3.8 14.1 - - - +
770C THR* 3.4 46.6 - - - +
771C SER 4.4 4.9 + - - +
772C LEU* 5.1 7.1 - - - +
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU* 4.4 11.5 - - + +
557B GLU 3.8 9.2 - - - +
558B LYS* 3.4 40.8 - - + +
559B LYS* 3.0 21.1 + - - +
560B THR* 2.9 37.3 + - - +
314C GLU* 1.3 77.2 + - + +
316C ALA* 1.3 60.0 + - - +
318C LEU* 4.1 15.1 + - + +
319C GLU* 4.1 20.6 - - - +
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Residues in contact with ALA 316 (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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556B LEU* 4.7 6.0 - - + +
558B LYS* 6.3 0.2 - - - +
313C CYS* 3.8 23.4 + - + -
314C GLU 3.2 1.0 - - - -
315C GLU* 1.3 77.6 - - - +
317C LYS* 1.3 61.2 + - - +
318C LEU 3.2 2.8 + - - -
319C GLU* 3.4 12.1 + - - +
320C ILE* 3.5 17.0 + - - +
357C LEU* 4.1 2.4 - - + +
473C ILE* 3.7 29.4 - - + +
474C PHE 5.0 2.2 - - - +
475C ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 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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307C PHE* 2.4 50.1 + - + +
308C LYS* 4.6 2.2 - - - +
310C VAL* 2.8 22.5 + - + +
311C ALA* 5.6 0.2 - - - -
313C CYS 3.3 16.1 + - - +
314C GLU* 3.3 35.5 + - - +
316C ALA* 1.3 77.4 - - - +
318C LEU* 1.3 64.4 + - - +
319C GLU 3.3 0.2 - - - -
320C ILE* 3.8 2.7 - - - +
321C MET* 3.1 35.9 + - - +
357C LEU* 3.8 27.3 - - + +
770C THR* 6.0 2.6 - - - +
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Residues in contact with LEU 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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534B ARG* 4.3 27.8 - - - +
314C GLU 3.4 11.6 + - - +
315C GLU* 4.2 14.8 - - + +
316C ALA 3.2 1.0 - - - -
317C LYS* 1.3 82.5 - - - +
319C GLU* 1.3 57.9 + - + +
320C ILE 3.2 0.4 - - - -
321C MET* 3.4 7.2 + - - +
322C GLU* 3.3 27.6 + - - +
772C LEU* 4.7 10.3 - - + -
773C PRO* 3.7 39.7 - - + -
776C LEU* 3.7 20.0 - - + -
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Residues in contact with GLU 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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534B ARG* 4.0 22.0 + - - +
551B ARG* 2.8 46.6 + - - -
556B LEU* 3.3 19.6 - - - +
315C GLU 4.1 8.4 - - - +
316C ALA 3.4 5.1 + - - +
317C LYS 3.3 0.2 - - - -
318C LEU* 1.3 77.8 - - + +
320C ILE* 1.3 64.6 + - - +
322C GLU* 4.2 4.0 - - - -
323C PHE* 3.9 14.0 - - - -
471C ARG* 3.3 33.8 + - - +
473C ILE* 3.6 20.2 - - + +
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Residues in contact with ILE 320 (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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307C PHE* 4.6 4.7 - - + -
316C ALA 3.5 15.7 - - - +
317C LYS* 3.5 6.4 + - - +
318C LEU 3.2 0.4 - - - -
319C GLU* 1.3 78.7 - - - +
321C MET* 1.3 65.3 + - - +
322C GLU 3.2 1.6 - - - -
323C PHE* 3.1 24.9 + - + +
324C VAL* 3.5 7.5 + - - +
346C LEU* 4.1 11.0 - - + -
357C LEU* 3.8 29.2 - - + +
361C THR* 3.3 27.6 - - + +
450C LEU* 3.9 33.0 - - + -
473C ILE* 3.7 23.3 - - + -
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Residues in contact with MET 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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307C PHE* 3.7 36.1 - - + -
317C LYS* 3.1 32.7 + - - +
318C LEU* 3.4 9.4 + - - +
320C ILE* 1.3 78.2 - - - +
322C GLU* 1.3 49.6 + - - +
324C VAL* 3.0 9.2 + - - +
325C ASN* 2.5 36.0 + - - +
772C LEU* 4.1 26.2 - - + -
776C LEU* 3.9 14.4 - - + +
779C TRP* 3.6 48.3 - - + -
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B LEU* 4.6 9.1 - - + +
534B ARG* 2.3 63.3 + - - +
318C LEU* 3.3 16.5 + - - +
320C ILE 3.2 0.8 - - - -
321C MET* 1.3 73.2 - - - +
323C PHE* 1.3 64.3 + - + +
325C ASN* 3.7 7.1 - - - +
326C PHE* 3.2 26.5 + - - +
333C TYR* 3.8 21.3 + - + +
341C PRO* 5.5 2.1 - - - +
471C ARG* 3.1 30.4 + - - +
776C LEU* 3.9 12.6 - - + +
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Residues in contact with PHE 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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319C GLU 3.9 18.6 - - - -
320C ILE* 3.1 18.8 + - + +
322C GLU* 1.3 79.6 - - + +
324C VAL* 1.3 63.1 + - + +
326C PHE* 3.6 4.1 + - - +
327C LEU* 3.4 31.0 + - - +
340C ILE* 6.0 0.4 - - + +
341C PRO* 3.5 37.2 - - + -
343C GLY 3.7 21.3 - - - -
344C ALA* 3.6 22.9 - - + -
361C THR* 5.8 1.1 - - + -
403C ILE* 5.0 6.3 - - + -
448C VAL* 3.6 35.7 - - + +
450C LEU* 3.6 20.0 - - + -
471C ARG* 4.4 14.6 - - - -
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Residues in contact with VAL 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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307C PHE* 4.4 14.4 - - + -
320C ILE 3.8 9.0 - - - +
321C MET* 3.0 7.9 + - - +
323C PHE* 1.3 74.6 - - + +
325C ASN* 1.3 65.2 + - - +
327C LEU* 3.4 4.6 + - - +
328C LYS* 3.0 32.3 + - + +
361C THR* 3.8 28.7 - - + -
364C GLU* 4.6 6.3 - - + +
365C ALA* 3.8 35.0 - - + +
403C ILE* 5.0 1.1 - - + -
779C TRP* 3.6 22.4 - - + -
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Residues in contact with ASN 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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321C MET 2.5 20.7 + - - +
322C GLU* 3.9 7.0 - - - -
323C PHE 3.4 0.2 - - - -
324C VAL* 1.3 73.7 - - - +
326C PHE* 1.3 56.3 + - - +
328C LYS* 4.8 1.3 - - - -
329C ASN* 3.0 32.1 + - - +
332C GLN* 3.7 7.1 + - - +
333C TYR* 3.1 23.9 + - - +
775C GLY 2.4 30.5 + - - +
776C LEU* 3.4 14.1 - - + +
778C ASP* 3.7 17.2 - - - +
779C TRP* 3.7 18.8 - - + -
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Residues in contact with PHE 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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530B LEU* 5.0 5.2 - - + -
322C GLU 3.2 19.9 + - - +
323C PHE* 4.0 4.7 - - - +
324C VAL 3.2 0.4 - - - -
325C ASN* 1.3 77.7 - - - +
327C LEU* 1.3 66.8 + - + +
330C PRO* 3.3 32.3 - - + +
333C TYR* 3.5 45.0 - + + -
334C GLN* 4.0 27.1 - - + -
338C ALA* 3.7 14.6 - - + -
339C LYS* 4.3 5.6 - - - -
340C ILE* 3.5 53.4 - - + -
341C PRO* 5.0 4.9 - - + -
446C ASN* 4.7 7.4 - - - -
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Residues in contact with LEU 327 (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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323C PHE 3.4 19.0 + - - +
324C VAL* 3.4 4.2 + - - +
326C PHE* 1.3 80.8 - - + +
328C LYS* 1.3 58.6 + - - +
330C PRO* 4.5 7.2 - - - +
340C ILE* 4.0 25.6 - - + -
365C ALA* 5.8 0.4 - - + -
367C VAL* 3.8 24.2 - - + +
401C PRO* 3.4 39.0 - - + +
403C ILE* 3.8 25.4 - - + -
446C ASN* 4.5 9.9 - - + +
448C VAL* 4.5 7.2 - - + -
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Residues in contact with LYS 328 (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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324C VAL* 3.0 24.4 + - + +
325C ASN* 4.4 1.8 - - - +
327C LEU* 1.3 80.0 - - - +
329C ASN* 1.3 79.6 + - - +
330C PRO* 3.7 6.7 - - - +
364C GLU* 4.9 11.4 + - - +
366C ASN* 5.2 14.5 - - + +
778C ASP* 4.2 22.5 + - + +
779C TRP* 4.9 15.3 - - + -
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Residues in contact with ASN 329 (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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325C ASN* 3.0 25.4 + - - +
326C PHE 3.5 3.0 - - - +
328C LYS* 1.3 96.0 - - - +
330C PRO* 1.3 65.7 - - - +
331C LYS* 3.2 5.6 + - + +
332C GLN* 3.8 20.7 + - + +
333C TYR* 3.9 9.5 - - - -
778C ASP* 2.4 35.8 + - - +
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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