Contacts of the helix formed by residues 362 - 377 (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 ASP 362 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ARG* 2.8 41.5 + - - -
362A ASP* 3.4 11.1 - - - +
357D ARG* 3.5 12.6 + - - +
360D GLY 3.7 1.2 + - - +
361D PHE* 1.3 84.3 - - - +
363D TRP* 1.3 64.6 + - - +
364D PRO* 3.2 9.0 - - - +
365D LEU* 2.8 44.6 + - + +
366D LEU* 3.1 22.7 + - - +
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Residues in contact with TRP 363 (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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42A ASP* 4.7 7.9 + - + +
43A GLY* 3.6 32.2 - - - +
44A LEU* 3.6 41.3 - - + -
78A PRO* 3.9 15.0 - - + -
79A VAL 5.0 4.9 - - - +
29D TYR* 5.7 0.4 - - - -
42D ASP* 5.9 1.0 + - - -
361D PHE* 3.5 25.6 - + - -
362D ASP* 1.3 69.0 + - - +
364D PRO* 1.3 75.5 - - + +
366D LEU* 3.1 26.2 + - + +
367D VAL* 3.0 26.9 + - - +
391D GLU* 3.9 25.1 - - + -
395D MET* 5.5 0.7 - - + -
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Residues in contact with PRO 364 (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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78A PRO* 3.8 12.3 - - + -
80A PRO 3.9 20.6 - - - +
81A SER* 4.0 9.9 - - - +
86A ILE* 3.9 16.4 - - + +
356A ILE* 4.3 5.8 - - + -
357A ARG* 3.4 32.1 - - + +
362D ASP* 3.2 18.4 - - - +
363D TRP* 1.3 93.9 - - + +
365D LEU* 1.3 55.2 + - - +
367D VAL* 3.4 0.5 + - - -
368D LYS* 2.9 30.8 + - - +
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Residues in contact with LEU 365 (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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356A ILE* 4.6 18.4 - - + +
357A ARG* 3.8 9.2 - - - +
354D ALA* 3.7 24.0 - - + -
357D ARG* 3.5 26.5 - - - +
362D ASP* 2.8 34.2 + - + +
364D PRO* 1.3 72.5 - - - +
366D LEU* 1.3 58.1 + - - +
368D LYS* 3.7 3.9 - - + +
369D ASP* 2.9 37.2 + - - +
611D ARG 5.2 1.8 - - - +
612D GLN* 6.2 0.7 - - - -
613D ARG* 4.0 34.1 - - + +
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Residues in contact with LEU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D PHE* 4.0 14.8 - - + -
362D ASP 3.1 16.2 + - - +
363D TRP* 3.1 40.6 + - + +
365D LEU* 1.3 76.7 - - - +
367D VAL* 1.3 64.2 + - + +
369D ASP* 3.2 6.6 + - + +
370D PHE* 3.1 51.7 + - + -
391D GLU 4.2 5.8 - - - +
392D VAL* 3.8 25.8 - - + -
395D MET* 3.7 23.8 - - + -
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Residues in contact with VAL 367 (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* 3.5 31.9 - - + -
76A ASP* 4.0 21.8 - - + +
78A PRO* 3.9 16.2 - - + -
86A ILE* 3.5 22.4 - - + -
363D TRP 3.0 15.3 + - - +
364D PRO 4.1 2.7 - - - +
366D LEU* 1.3 75.9 - - + +
368D LYS* 1.3 63.6 + - - +
370D PHE* 3.2 2.9 + - - +
371D ASN* 2.9 31.9 + - - +
395D MET* 4.4 13.0 - - + -
399D TYR* 4.7 5.2 - - - +
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Residues in contact with LYS 368 (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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85A ASP 2.9 25.6 + - - +
86A ILE* 3.2 21.0 + - + +
87A SER 3.6 7.3 + - - -
88A GLN* 2.7 31.4 + - - +
356A ILE* 3.7 35.7 - - + -
364D PRO 2.9 18.5 + - - +
365D LEU* 3.7 5.4 - - - +
367D VAL* 1.3 76.7 - - - +
369D ASP* 1.3 64.9 + - - +
371D ASN* 3.2 2.3 + - - -
372D LEU* 2.9 26.3 + - + +
613D ARG* 4.0 29.8 - - + -
614D GLN* 4.9 4.9 - - - +
552E ASP 4.3 6.9 + - - -
553E PRO* 5.6 0.2 - - - +
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Residues in contact with ASP 369 (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* 2.8 32.2 + - - +
365D LEU* 2.9 22.6 + - - +
366D LEU* 3.2 6.9 + - + +
368D LYS* 1.3 77.2 - - - +
370D PHE* 1.3 61.0 + - + +
372D LEU* 3.1 4.8 + - - +
373D LEU* 2.9 31.1 + - - +
589D PHE* 3.6 18.8 - - + -
613D ARG* 2.8 47.1 + - - +
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Residues in contact with PHE 370 (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* 6.0 1.6 - - - -
366D LEU* 3.1 43.2 + - + +
367D VAL 3.8 5.6 - - - +
369D ASP* 1.3 80.7 - - + +
371D ASN* 1.3 62.2 + - - +
373D LEU* 3.2 17.7 + - + +
374D ARG* 3.0 29.9 + - + +
381D PHE* 4.0 10.5 - + - -
392D VAL* 3.8 8.1 - - + -
395D MET* 3.7 34.1 - - + -
396D CYS* 3.6 39.7 - - - -
399D TYR* 4.0 27.1 - + + -
401D ILE* 3.9 19.3 - - + -
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Residues in contact with ASN 371 (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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75A VAL* 6.2 0.2 - - - +
76A ASP 5.4 1.2 + - - -
86A ILE* 3.0 41.0 + - - +
87A SER* 3.7 16.0 - - - +
88A GLN* 4.2 10.1 - - + +
367D VAL* 2.9 23.8 + - - +
368D LYS 3.2 6.9 + - - +
370D PHE* 1.3 76.8 - - - +
372D LEU* 1.3 56.8 + - - +
374D ARG* 3.4 20.7 + - - +
375D TRP* 3.0 28.9 + - - +
399D TYR* 4.6 6.8 + - - -
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Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 3.5 34.8 - - + +
368D LYS* 2.9 20.1 + - - +
369D ASP 3.4 7.2 - - - +
371D ASN* 1.3 74.6 - - - +
373D LEU* 1.3 58.9 + - - +
375D TRP* 3.3 9.6 + - + +
376D LEU* 2.8 32.5 + - - +
589D PHE* 3.9 19.7 - - + -
609D PHE* 3.5 31.8 - - + -
613D ARG* 3.7 46.9 - - + +
615D PRO* 5.8 1.8 - - + -
552E ASP* 5.9 0.2 - - + -
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Residues in contact with LEU 373 (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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348D VAL* 3.7 31.2 - - + -
350D LYS* 4.4 9.4 - - + -
369D ASP 2.9 20.5 + - - +
370D PHE* 3.2 28.0 + - + +
372D LEU* 1.3 72.8 - - - +
374D ARG* 1.3 61.6 + - - +
376D LEU* 3.3 3.3 + - + +
377D GLY 3.2 2.9 + - - -
378D ALA* 3.0 46.7 + - + +
380D ALA 5.1 0.7 - - - +
381D PHE* 3.8 32.5 - - + -
401D ILE* 4.3 15.7 - - + -
589D PHE* 3.9 15.9 - - + -
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Residues in contact with ARG 374 (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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75A VAL* 5.1 14.5 - - - +
291D TYR* 2.7 58.1 + - + +
370D PHE 3.0 19.4 + - - +
371D ASN* 4.0 15.1 + - - +
373D LEU* 1.3 73.5 - - - +
375D TRP* 1.3 65.7 + - - +
377D GLY 3.2 7.8 + - - -
399D TYR* 3.5 47.8 + - + +
401D ILE* 4.7 7.4 - - + -
627D TRP* 3.4 6.6 - - - -
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Residues in contact with TRP 375 (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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88A GLN* 3.8 29.4 - - + -
90A TRP* 6.0 1.2 - - - +
371D ASN 3.0 18.6 + - - +
372D LEU* 3.5 8.3 - - + +
374D ARG* 1.3 74.9 - - - +
376D LEU* 1.3 75.6 + - + +
609D PHE* 3.8 34.3 - + - -
615D PRO* 4.2 10.3 - - + -
619D ALA* 4.4 9.2 - - + -
620D PHE* 3.5 39.9 - + - -
623D ARG* 3.0 58.6 + - - +
627D TRP* 2.9 22.8 + - - -
552E ASP* 3.3 23.6 + - - -
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Residues in contact with LEU 376 (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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348D VAL* 3.6 31.6 - - + -
372D LEU 2.8 17.8 + - - +
373D LEU* 3.5 9.0 - - + +
375D TRP* 1.3 90.5 - - + +
377D GLY* 1.3 58.2 + - - +
378D ALA* 3.9 11.0 - - + +
608D ILE* 3.7 24.5 - - + -
609D PHE* 4.5 9.6 - - + -
619D ALA 3.6 24.5 - - - +
622D LEU* 4.4 3.8 - - + -
623D ARG* 3.3 30.7 - - + +
626D TYR* 3.4 19.4 - - + +
627D TRP* 3.6 2.0 - - - -
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Residues in contact with GLY 377 (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 TYR* 4.4 0.7 - - - -
292D LEU* 3.8 13.1 - - - +
346D HIS* 2.9 32.2 + - - -
373D LEU 3.2 0.4 + - - -
374D ARG 3.2 7.4 + - - -
375D TRP 3.2 5.3 + - - -
376D LEU* 1.3 80.8 - - - +
378D ALA* 1.3 61.8 + - - +
626D TYR* 3.5 7.1 - - - +
627D TRP* 3.4 22.9 - - - -
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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