Contacts of the helix formed by residues 314 - 324 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312D ALA 4.4 0.2 - - - +
313D ARG* 1.3 79.5 - - - +
315D GLN* 1.3 58.8 + - - +
317D LEU* 3.2 24.1 + - - +
318D LYS* 2.9 32.1 + - - +
423D ASP* 2.9 19.6 + - - -
426D LYS* 3.6 19.1 - - - +
427D ILE* 3.4 23.0 - - - +
430D GLU* 3.5 10.5 + - - -
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Residues in contact with GLN 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D ARG 4.8 1.6 + - - +
314D SER* 1.3 69.9 - - - +
316D GLN* 1.3 67.2 + - - +
318D LYS* 3.8 33.5 - - - +
319D SER* 3.0 25.6 + - - -
322D ARG* 4.5 6.6 + - - -
430D GLU* 2.8 21.4 + - - +
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Residues in contact with GLN 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D SER* 4.1 2.9 - - - +
315D GLN* 1.3 75.4 - - - +
317D LEU* 1.3 65.8 + - + +
319D SER* 3.0 19.1 + - - -
320D LEU* 3.0 14.6 + - + +
340D MET 5.0 6.2 - - - +
426D LYS* 2.9 28.3 + - + +
429D GLU* 3.4 24.0 + - - +
430D GLU* 2.7 43.1 + - + +
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Residues in contact with LEU 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D MET* 3.6 13.6 - - + +
312D ALA* 3.8 14.4 - - + -
314D SER* 3.2 14.6 + - - +
316D GLN* 1.3 79.7 - - + +
318D LYS* 1.3 64.0 + - - +
319D SER 2.8 6.5 + - - -
320D LEU* 3.3 22.0 + - + +
321D GLY 3.2 19.1 + - - -
340D MET* 4.4 9.6 - - + +
419D LEU* 4.1 15.0 - - + -
422D TRP* 3.3 39.7 - - + +
423D ASP* 3.5 31.9 - - + +
426D LYS* 4.4 4.3 - - + -
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Residues in contact with LYS 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D MET 4.6 5.8 - - - +
309D LEU* 5.8 3.0 - - - +
312D ALA* 3.2 26.1 - - - +
313D ARG* 2.9 29.9 + - - +
314D SER 2.9 21.2 + - - +
315D GLN* 3.8 30.7 - - - +
316D GLN 3.5 0.2 - - - -
317D LEU* 1.3 75.8 - - - +
319D SER* 1.3 58.2 + - - +
321D GLY* 4.2 1.3 + - - -
322D ARG* 3.5 26.3 + - + +
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Residues in contact with SER 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D GLN 3.0 17.4 + - - -
316D GLN* 3.0 9.1 + - - -
317D LEU 2.8 1.8 - - - -
318D LYS* 1.3 75.9 - - - +
320D LEU* 1.3 66.9 + - - +
321D GLY 3.1 0.9 - - - -
322D ARG* 2.8 37.6 + - - +
323D LEU* 2.7 38.5 + - - +
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Residues in contact with LEU 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D MET* 3.7 11.0 - - + -
316D GLN* 3.0 11.8 + - + +
317D LEU* 3.3 15.2 + - + +
319D SER* 1.3 79.7 + - - +
321D GLY* 1.3 57.1 + - - +
323D LEU* 2.8 6.6 + - + +
324D SER* 2.6 43.2 + - - +
335D MET* 3.9 40.8 - - + +
336D VAL* 5.1 0.7 - - - -
339D GLY* 4.1 8.1 - - - +
340D MET* 3.1 49.8 - - + +
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Residues in contact with GLY 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D VAL* 4.1 12.8 - - - -
308D MET* 3.2 18.8 - - - +
309D LEU* 4.1 14.7 - - - +
317D LEU 3.2 11.4 + - - -
318D LYS 4.4 1.6 - - - -
319D SER 3.1 1.2 - - - -
320D LEU* 1.3 79.3 - - - +
322D ARG* 1.3 63.1 + - - +
324D SER 3.4 2.3 + - - -
325D ILE* 3.4 23.6 + - - +
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Residues in contact with ARG 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D LEU* 4.6 9.6 - - + +
315D GLN* 4.5 7.7 + - - -
318D LYS* 3.5 18.1 + - + +
319D SER* 2.8 53.6 + - - +
321D GLY* 1.3 73.3 - - - +
323D LEU* 1.3 68.5 + - + +
324D SER 3.5 0.3 + - - -
325D ILE* 4.2 10.1 + - - +
326D ALA 5.4 0.2 + - - -
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Residues in contact with LEU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D SER* 2.7 33.3 + - - +
320D LEU* 2.8 8.9 + - + +
322D ARG* 1.3 83.7 - - - +
324D SER* 1.3 59.5 + - - +
325D ILE 3.9 0.9 - - - -
327D PRO* 3.8 11.8 - - - +
335D MET* 3.8 29.3 - - + +
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Residues in contact with SER 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D THR* 5.9 0.2 - - - +
305D VAL* 3.4 22.0 - - - +
320D LEU* 2.6 28.5 + - - +
323D LEU* 1.3 73.4 - - - +
325D ILE* 1.3 62.3 + - - +
327D PRO* 3.5 9.9 - - - -
328D GLY* 3.8 9.0 + - - -
332D ILE 6.1 0.4 - - - -
333D ASN* 6.2 0.7 - - - -
335D MET* 3.1 35.8 - - - +
336D VAL* 3.3 22.8 - - - +
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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