Contacts of the helix formed by residues 309 - 324 (chain C) in PDB entry 3GZN
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 PRO 309 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C ARG* 3.5 40.2 - - - +
307C GLN 4.3 2.5 - - - +
308C THR* 1.4 93.8 - - + +
310C SER* 1.3 65.5 + - - +
311C PHE* 3.2 7.2 - - + +
312C TRP* 3.0 24.9 + - + -
313C ILE* 3.3 10.9 + - - +
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Residues in contact with SER 310 (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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309C PRO* 1.3 72.0 - - - +
311C PHE* 1.3 61.8 + - - +
313C ILE* 3.6 10.7 - - - +
314C LEU* 3.3 30.6 + - - +
382C ILE* 3.9 24.3 - - - +
386C GLU* 5.1 4.2 + - - -
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Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C PRO* 3.6 35.2 - - + +
178C VAL 4.1 12.3 - - - -
179C ILE* 3.7 36.3 - - + -
295C ILE* 4.7 14.1 - - + -
309C PRO* 3.1 5.1 + - + +
310C SER* 1.3 78.8 - - - +
312C TRP* 1.3 93.4 + + + +
314C LEU* 3.3 12.2 + - - +
315C ALA* 2.9 27.8 + - + +
390C LEU* 5.5 1.7 - - + +
397C LEU* 4.5 10.5 - - + -
399C VAL* 3.7 26.2 - - + -
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Residues in contact with TRP 312 (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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175C GLU* 2.8 24.3 + - - -
177C PRO* 5.4 1.1 - - + -
295C ILE* 3.7 34.1 - - + -
298C ASP* 3.7 18.4 - - + -
300C ARG* 3.1 43.6 - - + +
301C CYS* 3.6 27.0 - - + -
304C ILE* 3.7 9.2 - - - +
308C THR* 3.7 19.7 - - + -
309C PRO* 3.0 14.8 + - + +
311C PHE* 1.3 90.9 - + + +
313C ILE* 1.3 67.9 + - - +
315C ALA* 3.4 9.8 + - + +
316C ARG* 3.2 13.9 + - - +
399C VAL* 4.2 18.2 - - + -
401C ARG* 3.3 24.5 - - - -
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Residues in contact with ILE 313 (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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304C ILE* 4.2 21.3 - - + -
305C THR 5.1 2.0 - - - +
308C THR* 3.8 22.9 - - + +
309C PRO 3.3 19.2 + - - +
310C SER* 3.6 10.3 - - - +
311C PHE 3.2 0.2 - - - -
312C TRP* 1.3 75.2 - - - +
314C LEU* 1.3 61.3 + - + +
316C ARG* 2.8 23.0 + - - +
317C ALA* 2.9 11.4 + - + +
368C VAL* 5.0 12.3 - - + +
371C LEU* 4.1 22.9 - - + +
372C LEU* 4.9 22.9 - - + -
375C ILE* 5.2 8.3 - - + -
377C GLN* 5.7 1.3 - - - +
382C ILE* 5.1 11.9 - - + -
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ILE* 4.3 15.3 - - + -
310C SER* 3.3 26.2 + - - +
311C PHE* 3.3 5.5 + - - +
313C ILE* 1.3 80.7 - - + +
315C ALA* 1.3 63.4 + - - +
317C ALA* 3.2 8.2 + - - +
318C LEU* 3.1 28.2 + - - +
368C VAL* 4.3 10.8 - - + -
382C ILE* 4.2 26.2 - - + -
386C GLU* 5.4 5.8 - - + +
387C LEU* 4.3 14.6 - - + -
390C LEU* 3.5 45.9 - - + +
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Residues in contact with ALA 315 (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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295C ILE* 4.2 15.5 - - + -
296C PHE* 3.5 10.5 - - - -
301C CYS* 3.7 8.4 - - - -
311C PHE* 2.9 20.7 + - + +
312C TRP* 3.4 34.1 - - + +
313C ILE 3.0 0.4 + - - -
314C LEU* 1.3 76.9 - - - +
316C ARG* 1.3 60.7 + - - +
318C LEU* 3.3 12.4 + - - +
319C LYS 3.2 14.9 + - - -
390C LEU* 5.1 0.6 - - - +
397C LEU* 5.6 3.8 - - + -
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Residues in contact with ARG 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C CYS* 3.2 29.7 + - - +
302C ILE* 2.7 34.8 + - - +
304C ILE* 4.2 13.5 - - + +
312C TRP 3.2 8.4 + - - +
313C ILE 2.8 8.8 + - - +
315C ALA* 1.3 76.5 - - - +
317C ALA* 1.3 55.0 + - - +
318C LEU 2.8 11.1 + - - -
319C LYS* 3.0 17.9 + - - +
320C GLU* 2.9 56.8 + - + +
371C LEU* 3.6 30.5 - - + +
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Residues in contact with ALA 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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313C ILE 2.9 12.9 + - - +
314C LEU* 3.2 11.8 + - - +
316C ARG* 1.3 73.4 - - - +
318C LEU* 1.3 58.1 + - - +
320C GLU* 4.4 1.6 - - - -
321C PHE* 3.8 13.2 + - - +
364C VAL* 3.5 28.6 - - + +
367C HIS* 4.0 26.8 - - + +
368C VAL* 4.1 20.6 - - + -
371C LEU* 3.7 9.3 - - + +
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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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296C PHE* 4.0 12.3 - - + -
314C LEU 3.1 16.6 + - - +
315C ALA* 3.4 9.4 - - - +
316C ARG 2.8 0.8 - - - -
317C ALA* 1.3 79.2 - - - +
319C LYS* 1.3 64.1 + - - +
320C GLU 3.3 1.1 - - - -
321C PHE* 3.4 5.8 + - + +
322C VAL* 3.1 26.0 + - - +
330C LEU* 4.8 3.5 - - + +
331C PRO* 4.0 31.5 - - + +
364C VAL* 4.3 11.9 - - + -
390C LEU* 3.8 29.4 - - + -
391C CYS* 4.7 3.6 - - - -
394C SER* 4.2 14.8 - - - +
397C LEU* 3.8 28.9 - - + -
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Residues in contact with LYS 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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296C PHE* 3.2 65.7 + - + +
297C ASN* 4.4 7.9 + - - -
301C CYS* 4.5 3.8 - - - -
302C ILE* 3.5 23.4 - - - +
315C ALA 3.2 8.1 + - - +
316C ARG* 3.0 26.8 + - - +
318C LEU* 1.3 76.8 - - - +
320C GLU* 1.3 64.5 + - - +
322C VAL* 3.1 16.6 + - + +
323C ALA* 3.2 12.5 + - - +
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Residues in contact with GLU 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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316C ARG* 2.9 57.1 + - + +
317C ALA* 4.8 0.2 - - - -
319C LYS* 1.3 79.9 - - - +
321C PHE* 1.3 58.2 + - - +
323C ALA* 3.2 13.1 + - - +
324C LYS* 3.0 28.9 + - - +
367C HIS* 3.1 30.5 - - + +
371C LEU* 5.0 8.1 - - + -
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Residues in contact with PHE 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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317C ALA 3.8 14.1 + - - +
318C LEU* 3.4 11.5 + - - +
320C GLU* 1.3 77.8 - - - +
322C VAL* 1.3 61.6 + - - +
324C LYS 3.3 6.5 + - - +
325C GLU* 3.9 19.5 - - + +
326C GLY* 3.0 46.6 + - - -
329C ASN 3.9 13.0 - - - -
330C LEU* 4.2 1.6 - - - -
331C PRO* 4.0 23.1 - - + -
356C LYS* 5.8 0.4 - - - -
360C ASP* 3.3 49.4 - - + -
363C ALA* 3.6 21.5 - - + -
364C VAL* 3.5 21.8 - - + -
367C HIS* 4.1 9.1 - + + +
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Residues in contact with VAL 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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288C ILE* 3.8 24.7 - - + -
296C PHE* 4.1 17.3 - - + -
318C LEU 3.1 15.5 + - - +
319C LYS* 3.1 12.2 + - + +
321C PHE* 1.3 76.1 - - + +
323C ALA* 1.3 61.0 + - - +
327C GLN 4.2 0.2 + - - -
328C GLY* 3.0 47.9 + - - +
329C ASN 3.9 17.5 - - - +
330C LEU* 4.3 6.3 - - + +
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Residues in contact with ALA 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 LYS 3.2 9.8 + - - +
320C GLU* 3.2 19.4 + - - +
322C VAL* 1.3 80.4 - - - +
324C LYS* 1.3 62.3 + - + +
327C GLN* 4.9 3.5 + - - -
328C GLY 5.1 0.2 + - - -
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Residues in contact with LYS 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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320C GLU 3.0 14.7 + - - +
321C PHE 3.3 0.4 + - - -
323C ALA* 1.3 78.9 - - + +
325C GLU* 1.3 74.7 + - - +
326C GLY 2.8 15.4 + - - -
327C GLN* 3.0 14.7 + - - -
367C HIS* 4.5 7.4 - - + -
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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