Contacts of the helix formed by residues 314 - 330 (chain C) in PDB entry 3QNQ
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 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C ARG* 1.3 77.9 + - - +
315C GLN* 1.3 59.8 + - - +
316C GLN* 3.8 4.1 - - - +
317C LEU* 3.2 28.4 + - - +
318C LYS* 3.1 31.9 + - - +
423C ASP* 2.8 26.5 + - - -
426C LYS* 4.3 6.2 - - - +
427C ILE* 3.6 16.8 - - - +
430C GLU* 3.6 17.3 - - - -
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Residues in contact with GLN 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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313C ARG 3.7 1.9 + - - +
314C SER* 1.3 71.9 - - - +
316C GLN* 1.3 57.4 + - - +
318C LYS* 3.7 31.0 - - - +
319C SER* 3.1 26.8 + - - -
322C ARG* 4.6 8.1 + - - -
430C GLU* 3.0 21.2 + - - +
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Residues in contact with GLN 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C SER* 3.8 6.7 - - - +
315C GLN* 1.3 77.4 - - - +
317C LEU* 1.3 72.6 + - + +
319C SER* 3.3 4.6 + - - -
320C LEU* 2.7 35.0 + - - +
340C MET 5.1 4.7 - - - +
426C LYS* 3.0 67.3 + - - +
429C GLU* 4.8 1.8 + - - +
430C GLU* 2.9 19.4 + - - +
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Residues in contact with LEU 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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308C MET* 3.8 28.6 - - + +
312C ALA* 4.0 11.9 - - + -
314C SER* 3.2 15.7 + - - +
316C GLN* 1.3 88.3 - - + +
318C LYS* 1.3 66.1 + - - +
320C LEU* 3.7 15.2 - - + +
321C GLY 3.0 18.5 + - - -
340C MET* 4.4 8.1 - - - +
419C LEU* 3.8 22.9 - - + -
422C TRP* 3.4 38.6 - - + +
423C ASP* 3.8 24.0 - - + -
426C LYS* 5.1 0.7 - - + -
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Residues in contact with LYS 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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308C MET 5.0 1.8 - - - -
309C LEU* 5.1 3.5 - - - +
312C ALA* 3.3 33.7 + - + +
313C ARG* 3.7 16.7 + - - +
314C SER 3.1 15.8 + - - +
315C GLN* 3.7 31.6 - - - +
317C LEU* 1.3 79.1 - - - +
319C SER* 1.3 63.5 + - - +
321C GLY* 3.4 1.4 + - - -
322C ARG* 3.3 37.1 + - + +
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Residues in contact with SER 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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315C GLN 3.1 19.2 + - - -
316C GLN* 3.6 5.8 - - - -
317C LEU 3.2 0.2 - - - -
318C LYS* 1.3 77.3 - - - +
320C LEU* 1.3 67.4 + - - +
322C ARG* 3.1 35.4 + - - +
323C LEU* 3.3 27.9 + - - +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C MET* 3.6 13.0 - - + -
316C GLN 2.7 21.8 + - - +
317C LEU* 3.7 13.2 - - + +
319C SER* 1.3 71.6 - - - +
321C GLY* 1.3 64.7 + - - +
323C LEU* 2.9 16.1 + - + -
324C SER* 2.8 23.7 + - - +
335C MET* 3.5 39.0 - - + +
336C VAL* 4.8 2.7 - - + -
339C GLY* 4.1 19.7 - - - +
340C MET* 4.1 31.4 - - + +
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Residues in contact with GLY 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL* 4.0 5.7 - - - +
308C MET* 3.2 22.3 - - - +
309C LEU* 3.8 16.6 - - - -
317C LEU 3.0 14.0 + - - -
318C LYS 3.8 2.0 - - - -
319C SER 3.2 0.2 - - - -
320C LEU* 1.3 77.5 - - - +
322C ARG* 1.3 57.3 + - - +
323C LEU 2.8 6.6 + - - -
324C SER* 3.1 9.6 + - - -
325C ILE* 3.1 17.7 + - - +
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LEU* 3.8 17.4 - - + +
315C GLN* 4.6 8.9 + - - -
318C LYS* 3.3 25.7 + - + +
319C SER* 3.1 42.7 + - - +
321C GLY* 1.3 73.7 - - - +
323C LEU* 1.3 71.4 + - + +
325C ILE* 4.0 12.5 - - - +
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Residues in contact with LEU 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 SER* 3.3 27.4 - - - +
320C LEU* 2.9 9.2 + - + +
322C ARG* 1.3 95.2 - - + +
324C SER* 1.3 59.0 + - - +
325C ILE* 3.6 1.3 - - - -
326C ALA* 5.1 1.2 - - - +
327C PRO* 3.6 15.1 - - - +
335C MET* 3.8 26.4 - - + +
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Residues in contact with SER 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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305C VAL* 4.1 9.1 - - - +
308C MET* 4.0 2.4 - - - +
320C LEU* 2.8 24.2 + - - +
321C GLY* 3.7 5.0 + - - -
323C LEU* 1.3 77.0 - - - +
325C ILE* 1.3 66.3 + - - +
327C PRO* 3.2 10.4 - - - +
328C GLY* 3.0 20.6 + - - -
332C ILE 4.8 0.9 - - - +
333C ASN* 6.5 0.2 - - - -
335C MET* 3.5 25.8 - - - -
336C VAL* 3.5 24.7 - - - +
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Residues in contact with ILE 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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302C LEU* 4.0 23.1 - - + -
305C VAL* 3.8 9.4 - - + -
306C VAL* 4.5 8.1 - - + -
309C LEU* 3.8 29.8 - - + -
321C GLY 3.1 18.6 + - - +
322C ARG* 4.0 16.8 - - - +
323C LEU 5.0 0.2 - - - -
324C SER* 1.3 75.0 - - - +
326C ALA* 1.3 67.6 + - + +
328C GLY* 2.8 3.9 + - - -
329C ILE* 2.6 51.0 + - + +
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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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323C LEU 5.0 1.3 + - - +
325C ILE* 1.3 85.2 - - + +
327C PRO* 1.3 71.6 - - + +
329C ILE* 3.2 14.5 - - - +
330C PHE* 3.1 27.9 - - + -
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Residues in contact with PRO 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 LEU 3.6 11.9 - - - +
324C SER* 3.2 30.1 - - - +
326C ALA* 1.3 96.7 - - + +
328C GLY* 1.3 53.4 + - - -
330C PHE* 3.2 15.7 + - + +
331C ASN 3.4 0.2 + - - -
332C ILE* 2.9 48.2 + - + +
335C MET* 4.5 12.6 - - + -
173D PRO* 5.3 10.8 - - + -
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Residues in contact with GLY 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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295C MET 4.3 0.5 - - - +
296C GLY* 3.7 12.8 - - - +
301C THR* 5.7 2.0 - - - -
302C LEU* 3.9 18.4 - - - +
305C VAL* 5.6 4.5 - - - -
324C SER 3.0 13.0 + - - -
325C ILE* 2.8 7.3 + - - -
327C PRO* 1.3 72.4 - - - +
329C ILE* 1.3 63.8 + - - +
330C PHE 2.9 2.0 - - - -
331C ASN* 2.9 16.2 + - - -
332C ILE 3.4 13.5 - - - -
333C ASN* 5.5 1.6 - - - -
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Residues in contact with ILE 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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302C LEU* 4.2 13.4 - - + +
325C ILE* 2.6 38.8 + - + +
326C ALA* 3.2 14.6 - - - +
328C GLY* 1.3 72.4 - - - +
330C PHE* 1.3 86.0 + - + +
331C ASN* 3.6 5.2 + - - -
385C PRO* 3.5 28.5 - - + +
386C ILE 4.2 2.4 + - - -
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Residues in contact with PHE 330 (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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326C ALA* 3.1 27.4 - - + -
327C PRO* 3.2 10.0 + - + +
328C GLY 2.9 0.8 - - - -
329C ILE* 1.3 93.6 - - + +
331C ASN* 1.3 70.7 + - - +
332C ILE* 3.2 16.9 + - + +
382C TRP* 4.1 0.5 - - - -
383C THR* 3.4 40.1 - - + +
385C PRO* 4.0 20.9 - - + -
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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