Contacts of the helix formed by residues 385 - 393 (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 PRO 385 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329D ILE* 3.3 31.0 - - + +
330D PHE* 4.4 20.2 - - + -
383D THR 3.6 7.4 - - - +
384D THR* 1.3 88.4 - - + +
386D ILE* 1.3 69.0 + - + +
387D LEU 3.0 2.8 + - - +
388D PHE* 3.4 21.3 + - + -
389D SER* 3.0 19.8 + - - -
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Residues in contact with ILE 386 (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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291D LEU 5.2 0.7 - - - +
295D MET* 3.2 47.3 - - + -
302D LEU* 4.0 29.6 - - + -
329D ILE* 4.3 3.2 + - + -
331D ASN* 4.5 8.6 - - - +
384D THR 3.2 5.0 + - - -
385D PRO* 1.3 70.8 - - + +
387D LEU* 1.3 81.6 + - + +
389D SER* 3.4 3.7 - - - -
390D GLY 3.3 3.8 + - - -
404D GLN* 2.5 47.4 + - + +
408D PHE* 4.3 19.3 - - + -
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Residues in contact with LEU 387 (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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385D PRO* 3.0 3.4 + - - +
386D ILE* 1.3 94.5 - - + +
388D PHE* 1.3 76.6 + - + +
391D TYR* 3.5 13.5 + - - +
401D VAL* 3.8 30.2 - - + +
404D GLN* 3.6 17.8 - - + +
405D LEU* 3.6 33.0 - - + -
408D PHE* 6.4 0.2 - - + -
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Residues in contact with PHE 388 (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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384D THR* 4.6 5.2 - - + -
385D PRO* 3.4 23.3 + - + +
387D LEU* 1.3 83.3 - - + +
389D SER* 1.3 60.0 - - - +
391D TYR* 3.3 11.1 + + + +
392D LEU* 2.9 47.9 + - + +
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Residues in contact with SER 389 (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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291D LEU* 3.0 37.3 - - - +
380D VAL* 4.5 1.9 - - - +
384D THR* 3.6 32.9 - - - +
385D PRO 3.0 19.2 + - - -
386D ILE* 3.4 6.9 - - - -
387D LEU 3.2 0.2 - - - -
388D PHE* 1.3 77.8 - - - +
390D GLY* 1.3 58.7 + - - +
392D LEU* 3.9 2.5 - - - +
393D GLY* 2.8 29.3 + - - -
404D GLN* 3.4 3.6 + - - -
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Residues in contact with GLY 390 (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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292D TRP* 3.7 20.9 - - - -
386D ILE 3.3 2.4 + - - -
388D PHE 3.3 0.2 - - - -
389D SER* 1.3 73.4 - - - +
391D TYR* 1.3 57.1 + - - +
394D SER* 2.7 29.5 + - - -
400D GLY* 4.0 3.7 - - - -
401D VAL 4.2 7.2 - - - -
404D GLN* 3.0 35.1 + - - +
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Residues in contact with TYR 391 (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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48D LEU* 4.6 10.6 - - + +
49D PRO* 5.3 1.9 - - - +
50D ILE* 4.0 21.8 - - - +
387D LEU 3.5 7.2 + - - +
388D PHE* 3.3 12.7 + - + +
390D GLY* 1.3 79.8 - - - +
392D LEU* 1.3 76.3 + - + +
394D SER* 3.7 1.0 + - - -
396D GLY* 2.9 67.0 + - - -
397D LYS 3.6 7.3 + - - -
398D ILE* 4.4 19.1 - - + -
401D VAL* 3.4 23.4 - - + +
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Residues in contact with LEU 392 (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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44D ILE* 4.5 35.7 - - + +
48D LEU* 4.7 14.4 - - + -
376D SER* 3.6 6.2 + - - -
378D ALA* 5.2 2.6 - - - +
380D VAL* 4.9 17.0 - - + -
384D THR* 5.3 7.6 - - + -
388D PHE* 2.9 32.1 + - + +
389D SER* 4.0 2.9 - - - +
391D TYR* 1.3 87.8 - - + +
393D GLY* 1.3 58.2 + - - +
394D SER 2.9 10.6 + - - -
395D GLY* 3.1 14.9 + - - +
396D GLY* 4.7 2.5 - - - +
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Residues in contact with GLY 393 (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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287D GLN* 5.3 1.8 - - - +
291D LEU* 3.8 19.0 - - - +
292D TRP* 4.0 8.3 - - - -
375D PRO* 3.0 13.5 - - - +
376D SER* 2.9 22.4 + - - -
378D ALA* 4.8 6.9 - - - +
380D VAL* 4.6 5.1 - - - +
389D SER 2.8 21.1 + - - -
390D GLY 3.8 0.2 + - - -
391D TYR 3.6 0.4 - - - -
392D LEU* 1.3 72.2 - - - +
394D SER* 1.3 58.0 + - - +
395D GLY 3.6 0.4 - - - -
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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