Contacts of the helix formed by residues 389 - 400 (chain D) in PDB entry 3D8F
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 ARG 389 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383D GLU* 3.1 50.7 + - - +
384D GLU* 3.2 26.8 - - + +
386D ALA* 2.9 16.0 + - + +
387D PRO 3.3 1.4 + - - -
388D GLY* 1.3 75.8 - - - +
390D SER* 1.3 65.4 + - - +
391D SER 3.6 0.2 - - - -
392D VAL* 3.4 10.8 + - + +
393D ALA* 3.1 18.7 + - + +
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Residues in contact with SER 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D MET* 5.2 0.9 - - - +
384D GLU 3.2 14.9 - - - +
385D LEU* 3.6 16.1 + - - +
386D ALA 2.6 17.0 + - - -
387D PRO* 4.0 8.7 - - - -
388D GLY 3.2 1.5 - - - -
389D ARG* 1.3 81.6 - - - +
391D SER* 1.3 62.2 + - - +
392D VAL 3.2 0.2 + - - -
393D ALA* 3.3 0.9 + - - +
394D VAL* 3.2 25.1 + - - +
452D VAL* 3.8 31.1 - - - +
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Residues in contact with SER 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D GLY* 4.6 8.2 + - - -
390D SER* 1.3 80.0 + - - +
392D VAL* 1.3 61.5 + - - +
394D VAL* 3.5 10.3 + - - +
395D ASN* 3.3 18.9 + - - +
453D TRP 6.1 0.9 - - - -
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Residues in contact with VAL 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D GLY 3.1 23.8 - - - +
389D ARG* 3.5 13.7 - - + +
390D SER 3.2 0.6 - - - -
391D SER* 1.3 77.2 - - - +
393D ALA* 1.3 59.4 + - - +
394D VAL 3.1 0.4 - - - -
395D ASN* 3.0 8.4 + - - +
396D ASN* 2.9 35.8 + - - +
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Residues in contact with ALA 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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380D MET* 4.5 7.6 - - + -
384D GLU* 3.6 43.1 - - + +
389D ARG* 3.1 12.3 + - + +
390D SER 3.3 1.1 + - - +
392D VAL* 1.3 79.2 - - - +
394D VAL* 1.3 57.1 + - - +
396D ASN* 3.6 13.3 - - + +
397D CYS* 3.0 36.8 + - - -
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Residues in contact with VAL 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D MET* 5.0 4.9 - - + -
390D SER 3.2 20.8 + - - +
391D SER* 3.7 9.0 - - - +
392D VAL 3.1 0.6 - - - -
393D ALA* 1.3 75.3 - - - +
395D ASN* 1.3 64.6 + - - +
397D CYS* 3.2 5.9 + - - +
398D ILE* 3.0 28.6 + - + +
452D VAL* 4.5 19.5 - - + -
453D TRP 4.6 7.9 - - - +
454D GLY* 4.6 15.5 - - - +
466D ALA* 3.8 28.3 - - + -
468D VAL* 4.6 10.8 - - + -
479D CYS* 4.3 7.4 - - - -
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Residues in contact with ASN 395 (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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391D SER 3.3 8.9 + - - +
392D VAL* 3.0 9.7 + - - +
394D VAL* 1.3 78.6 - - - +
396D ASN* 1.3 61.4 + - - +
398D ILE* 3.9 19.2 - - - +
399D ARG* 3.0 65.5 + - - +
455D VAL 4.3 3.2 + - - -
456D GLY 2.8 31.2 + - - +
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Residues in contact with ASN 396 (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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392D VAL* 2.9 26.3 + - - +
393D ALA* 3.6 14.7 - - + +
395D ASN* 1.3 77.4 - - - +
397D CYS* 1.3 58.8 + - - +
399D ARG* 4.3 6.9 - - - +
400D GLN* 3.2 32.4 + - - +
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Residues in contact with CYS 397 (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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378D VAL* 3.8 43.3 - - + +
379D GLU 4.4 0.4 - - - -
380D MET* 3.9 25.1 - - - -
384D GLU* 6.5 0.2 - - - -
393D ALA* 3.0 25.3 + - - +
394D VAL 3.2 1.5 + - - +
396D ASN* 1.3 76.7 - - - +
398D ILE* 1.3 64.4 + - - +
400D GLN* 3.6 13.8 - - - +
401D LEU* 3.9 9.7 - - - +
479D CYS* 3.4 28.0 - - - -
481D VAL* 4.5 1.8 - - + -
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Residues in contact with ILE 398 (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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375D LEU* 6.0 0.2 - - - +
394D VAL* 3.0 31.1 + - + +
395D ASN* 3.2 15.5 + - - +
397D CYS* 1.3 72.8 - - - +
399D ARG* 1.3 60.4 + - + +
400D GLN 3.0 4.0 - - - -
401D LEU* 2.8 23.6 + - - +
402D SER* 2.9 15.3 + - - +
454D GLY 4.6 3.4 - - - +
455D VAL 3.2 29.6 - - - +
456D GLY* 5.6 2.2 - - - -
462D GLU 5.8 0.4 - - - +
464D ASP* 3.9 33.0 - - + +
466D ALA* 3.7 30.7 - - + +
481D VAL* 4.2 17.6 - - + +
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Residues in contact with ARG 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D ASN* 3.0 50.7 + - - +
396D ASN* 4.8 6.8 - - - +
398D ILE* 1.3 74.5 - - + +
400D GLN* 1.3 56.3 + - - +
401D LEU 3.1 4.8 + - - -
402D SER* 3.5 24.1 + - - +
456D GLY 5.4 1.5 + - - -
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Residues in contact with GLN 400 (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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378D VAL* 4.0 29.8 - - + +
396D ASN* 3.2 22.9 + - - +
397D CYS* 3.6 10.3 - - - +
398D ILE 2.9 1.2 + - - -
399D ARG* 1.3 75.3 - - - +
401D LEU* 1.3 68.9 + - + +
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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