Contacts of the helix formed by residues 345 - 357 (chain C) in PDB entry 6GL7
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 345 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275C CYS* 2.5 36.4 + - - +
277C ALA* 3.4 22.8 - - + +
284C SER* 3.6 1.2 - - - -
340C ARG 3.7 1.3 - - - +
341C ASP* 3.2 27.9 + - - +
342C PHE 4.8 0.8 - - - +
343C THR 3.4 4.0 + - - -
344C GLU* 1.3 76.0 - - - +
346C PRO* 1.3 67.5 - - - +
347C CYS* 2.8 28.4 + - - +
348C LEU* 3.3 12.9 + - + +
349C ARG* 3.2 22.6 + - - +
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Residues in contact with PRO 346 (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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277C ALA* 4.6 5.2 - - + -
282C VAL 5.5 1.8 - - - +
283C THR* 3.6 4.5 - - - +
284C SER* 3.5 22.7 - - - +
344C GLU 3.4 10.1 - - - +
345C ASN* 1.3 87.6 - - - +
347C CYS* 1.3 52.2 + - - +
349C ARG* 3.8 16.4 - - + +
350C ASN* 2.7 50.9 + - - +
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Residues in contact with CYS 347 (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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274C ASN 4.3 3.1 - - - -
275C CYS* 4.9 0.4 - - - -
283C THR 3.0 15.1 + - - +
284C SER* 3.5 9.6 - - - +
285C CYS* 2.1 48.7 - - - -
293C CYS* 3.5 29.4 - - - -
345C ASN* 2.8 23.2 + - - +
346C PRO* 1.3 75.7 - - - +
348C LEU* 1.3 53.4 + - - +
350C ASN* 4.1 0.4 - - - +
351C ALA* 2.6 40.9 + - - +
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Residues in contact with LEU 348 (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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221C PHE* 6.0 0.4 - - + -
271C PHE* 4.2 5.6 - - + -
293C CYS* 3.3 30.1 - - - -
294C LEU* 5.8 1.1 - - - +
297C TYR* 3.5 31.6 - - + -
319C VAL* 4.0 11.0 - - + -
341C ASP 3.2 27.6 - - - +
342C PHE* 3.6 23.3 - - - +
345C ASN* 3.3 8.5 + - + +
347C CYS* 1.3 79.2 - - - +
349C ARG* 1.3 58.3 + - + +
351C ALA* 4.2 4.3 - - + -
352C ILE* 2.8 53.8 + - + +
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Residues in contact with ARG 349 (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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317C ILE* 4.4 20.7 + - - +
318C VAL* 5.4 7.6 - - - +
342C PHE 5.9 1.3 - - - +
343C THR 2.5 32.3 + - - +
344C GLU* 2.9 36.8 + - - +
345C ASN 3.2 17.8 + - - +
346C PRO* 3.7 12.2 - - + +
348C LEU* 1.3 77.5 - - + +
350C ASN* 1.3 65.4 + - - +
352C ILE* 4.5 0.6 - - - +
353C GLN* 3.1 41.7 + - - +
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Residues in contact with ASN 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C VAL 5.0 2.2 + - - -
283C THR* 4.4 16.1 - - - +
290C TYR* 3.7 23.4 + - + +
346C PRO* 2.7 37.7 + - - +
349C ARG* 1.3 75.3 - - - +
351C ALA* 1.3 59.6 + - - +
353C GLN* 4.1 10.5 - - - +
354C ALA* 2.7 34.1 + - - +
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Residues in contact with ALA 351 (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 CYS* 4.7 1.6 - - - -
290C TYR* 3.4 33.3 - - + +
293C CYS* 5.3 2.5 - - + -
294C LEU* 5.7 1.1 - - + +
347C CYS* 2.6 29.2 + - - +
348C LEU* 4.0 4.9 - - + +
350C ASN* 1.3 73.0 - - - +
352C ILE* 1.3 54.6 + - + +
354C ALA* 3.1 1.2 + - - +
355C PHE* 2.6 55.5 + - + -
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Residues in contact with ILE 352 (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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221C PHE* 3.7 44.4 - - + +
294C LEU* 5.7 1.8 - - + -
297C TYR* 5.0 0.9 - - + -
309C TYR* 4.0 8.1 - - + +
317C ILE* 3.7 42.0 - - + +
319C VAL* 4.3 18.8 - - + -
348C LEU* 2.8 49.2 + - + +
349C ARG 4.5 0.2 - - - +
351C ALA* 1.3 71.9 - - + +
353C GLN* 1.3 51.9 + - - +
355C PHE* 3.7 7.9 - - + +
356C GLY* 2.7 32.6 + - - -
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Residues in contact with GLN 353 (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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223C SER* 5.5 1.0 - - - -
315C THR* 3.7 19.3 + - - +
316C GLY* 5.2 1.4 - - - -
317C ILE* 4.2 29.4 + - + +
349C ARG* 3.1 29.4 + - - +
350C ASN* 4.1 11.2 - - - +
352C ILE* 1.3 76.1 - - - +
354C ALA* 1.3 62.5 + - - +
356C GLY* 3.3 2.6 + - - -
357C ASN* 3.0 34.0 + - - +
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Residues in contact with ALA 354 (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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290C TYR* 4.2 15.9 - - + +
350C ASN 2.7 24.6 + - - +
351C ALA* 3.6 2.9 - - - +
353C GLN* 1.3 73.2 - - - +
355C PHE* 1.3 61.4 + - + +
357C ASN* 3.1 14.7 + - - +
358C GLY 3.1 1.0 + - - -
359C THR* 2.8 47.0 + - + +
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Residues in contact with PHE 355 (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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141C LEU* 3.4 23.1 - - + -
144C ILE* 3.7 27.1 - - + +
217C TYR* 6.2 2.5 - - + -
221C PHE* 4.2 13.1 - - + +
290C TYR* 3.5 48.2 - + + -
291C GLN* 3.7 2.2 - - - -
294C LEU* 3.6 36.8 - - + -
351C ALA* 2.6 36.5 + - + +
352C ILE* 3.7 7.2 - - + +
354C ALA* 1.3 69.7 - - - +
356C GLY* 1.3 65.5 + - - +
358C GLY* 3.0 13.9 + - - -
359C THR* 3.3 20.1 - - + +
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Residues in contact with GLY 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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221C PHE 3.4 19.4 + - - -
222C CYS* 4.2 1.3 - - - -
223C SER* 3.1 37.6 + - - -
352C ILE 2.7 19.7 + - - -
353C GLN* 3.3 3.3 + - - -
355C PHE* 1.3 72.4 - - - +
357C ASN* 1.3 57.4 + - - +
358C GLY 3.6 0.5 + - - -
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Residues in contact with ASN 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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223C SER* 4.3 10.4 + - - -
353C GLN* 3.0 25.1 + - - +
354C ALA* 3.1 8.7 + - - +
356C GLY* 1.3 79.1 - - - +
358C GLY* 1.3 59.1 + - - +
359C THR* 5.0 2.4 + - - +
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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