Contacts of the helix formed by residues 389 - 400 (chain D) in PDB entry 3HN3
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 ALA 389 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D ARG* 3.4 28.2 - - + +
352D GLU* 2.8 18.0 + - - +
361D PHE* 3.9 24.0 - - + -
388D TYR* 1.3 75.3 - - - +
390D GLU* 1.3 65.2 + - - +
391D GLU* 3.5 16.2 - - - +
392D VAL* 3.0 24.4 + - + +
393D MET* 3.5 4.0 + - - +
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Residues in contact with GLU 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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29D TYR* 3.7 39.2 - - + -
122D ARG* 4.0 7.1 + - - -
124D GLY* 4.6 8.2 - - - +
148D PRO* 3.6 27.9 - - - +
216D ARG* 4.6 8.3 - - - +
388D TYR 3.5 1.3 + - - -
389D ALA* 1.3 75.0 - - - +
391D GLU* 1.3 63.3 + - - +
393D MET* 2.8 26.0 + - - +
394D GLN* 2.9 18.2 + - + +
436D ARG* 3.6 39.6 + - + +
437D ASP* 5.0 1.3 - - - +
440D HIS* 4.6 5.3 - - + +
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Residues in contact with GLU 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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29D TYR* 3.1 31.6 + - + +
216D ARG* 5.7 1.4 - - - +
217D SER* 3.7 22.2 + - - -
361D PHE* 3.7 36.5 - - + -
363D TRP* 3.9 27.0 - - + -
366D LEU* 4.4 2.9 - - + -
389D ALA* 3.1 8.1 - - - +
390D GLU* 1.3 90.0 + - - +
392D VAL* 1.3 57.4 + - - +
394D GLN* 3.5 13.0 + - - +
395D MET* 3.1 33.7 + - - +
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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
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350D LYS* 6.3 0.4 - - + -
352D GLU* 4.4 4.9 - - + +
361D PHE* 5.0 5.4 - - + -
366D LEU* 3.8 22.0 - - + -
370D PHE* 4.3 9.4 - - + -
381D PHE* 3.8 20.0 - - + -
388D TYR* 4.0 24.5 - - + -
389D ALA* 3.0 24.4 + - + +
391D GLU* 1.3 76.8 - - - +
393D MET* 1.3 71.9 + - + +
395D MET* 3.3 4.4 + - - +
396D CYS* 3.0 26.3 + - - -
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Residues in contact with MET 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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381D PHE* 4.4 0.9 - - + -
383D THR* 4.1 17.7 - - + -
388D TYR* 4.7 4.3 - - + +
389D ALA 4.2 7.0 - - - +
390D GLU* 2.8 9.4 + - - +
392D VAL* 1.3 96.4 - - + +
394D GLN* 1.3 65.0 + - - +
396D CYS* 3.2 17.8 + - - +
397D ASP* 3.1 26.3 + - - +
403D VAL* 4.0 25.4 - - + -
405D ASP* 4.5 4.5 - - - +
436D ARG* 4.2 9.4 - - - +
437D ASP* 4.1 18.6 - - - +
440D HIS* 3.5 28.0 - - + +
442D ALA* 4.8 0.3 - - - +
443D VAL* 4.2 13.2 - - - -
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Residues in contact with GLN 394 (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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29D TYR* 2.7 53.7 - - - +
323D PRO* 6.6 0.2 - - + -
390D GLU* 2.9 18.5 + - - +
391D GLU* 3.6 14.0 - - - +
393D MET* 1.3 75.7 - - - +
395D MET* 1.3 63.3 + - + +
397D ASP* 3.3 8.2 + - - +
398D ARG* 3.2 33.1 + - - +
440D HIS* 4.0 15.5 - - + -
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Residues in contact with MET 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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44A LEU* 3.9 17.9 - - + -
76A ASP* 3.8 3.8 - - - +
363D TRP* 5.5 0.4 - - + -
366D LEU* 3.7 24.5 - - + -
367D VAL* 4.4 13.5 - - + -
370D PHE* 3.7 35.7 - - + -
391D GLU 3.1 16.5 + - - +
392D VAL 3.5 8.7 - - - +
393D MET 3.2 0.2 - - - -
394D GLN* 1.3 74.8 - - + +
396D CYS* 1.3 60.0 + - - +
398D ARG* 3.0 25.7 + - - +
399D TYR* 2.8 65.0 + - + +
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Residues in contact with CYS 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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370D PHE* 3.6 10.5 - - - -
381D PHE* 3.4 37.2 - - - -
392D VAL 3.0 18.9 + - - -
393D MET* 3.2 13.9 + - - +
395D MET* 1.3 76.1 - - - +
397D ASP* 1.3 57.4 + - - +
399D TYR 4.6 0.2 - - - +
400D GLY* 2.9 27.9 + - - -
401D ILE 3.2 23.1 + - - +
403D VAL* 3.4 17.7 - - + -
442D ALA* 3.5 13.4 - - + +
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Residues in contact with ASP 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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288D TRP* 3.0 25.9 + - - +
298D ALA* 3.4 6.2 - - - +
300D LEU* 3.8 16.4 - - + +
323D PRO* 5.3 7.5 - - + +
393D MET 3.1 12.8 + - - +
394D GLN* 3.5 9.5 - - - +
395D MET 3.2 0.4 - - - -
396D CYS* 1.3 76.2 - - - +
398D ARG* 1.3 61.4 + - + +
439D ASN 4.8 0.2 - - - +
440D HIS* 2.6 30.9 + - - +
441D PRO* 3.2 23.4 - - + +
442D ALA* 2.9 34.3 + - - +
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Residues in contact with ARG 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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44A LEU* 3.8 10.4 - - - +
76A ASP* 2.9 43.7 + - - -
298D ALA* 3.2 16.0 - - - +
300D LEU* 3.8 21.5 - - + -
394D GLN* 3.2 18.3 + - - +
395D MET* 3.0 24.8 + - - +
397D ASP* 1.3 79.0 - - + +
399D TYR* 1.3 64.9 + - + +
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Residues in contact with TYR 399 (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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76A ASP* 2.5 43.3 + - - +
291D TYR* 3.4 20.8 - - - +
297D PRO* 4.9 4.1 - - - +
298D ALA* 4.0 3.4 - - - -
367D VAL* 4.7 5.7 - - - +
370D PHE* 4.0 24.0 - + + -
371D ASN* 4.6 8.2 + - - -
374D ARG* 3.5 53.6 + - + +
395D MET* 2.8 49.8 + - + +
398D ARG* 1.3 83.7 - - + +
400D GLY* 1.3 62.3 + - - +
401D ILE* 3.4 17.9 + - + +
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Residues in contact with GLY 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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288D TRP* 3.7 20.6 - - - -
290D PRO* 3.4 9.0 - - - +
291D TYR* 2.8 30.5 + - - +
298D ALA* 3.5 11.0 - - - +
379D ASN 3.9 1.9 - - - +
396D CYS 2.9 8.1 + - - -
398D ARG 3.5 2.4 - - - -
399D TYR* 1.3 79.2 - - - +
401D ILE* 1.3 61.5 + - - +
402D VAL 3.6 2.6 + - - -
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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