Contacts of the helix formed by residues 362 - 377 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B ARG* 2.8 43.8 + - - -
362B ASP* 3.5 10.4 - - - +
357E ARG* 3.6 22.6 + - - +
360E GLY 3.6 1.5 + - - +
361E PHE* 1.3 87.3 - - - +
363E TRP* 1.3 58.6 + - - +
364E PRO* 3.4 6.9 - - - +
365E LEU* 3.0 31.6 + - + +
366E LEU* 3.1 27.4 + - - +
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Residues in contact with TRP 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 4.7 5.7 - - + +
43B GLY* 3.6 32.7 - - - +
44B LEU* 3.5 42.2 - - + -
78B PRO* 3.9 14.8 - - + -
79B VAL 5.0 4.3 - - - +
80B PRO* 6.2 1.1 - - + -
29E TYR* 5.6 0.9 - - - -
361E PHE* 3.5 21.6 - + - -
362E ASP* 1.3 69.1 + - - +
364E PRO* 1.3 75.7 - - + +
366E LEU* 3.1 29.9 + - + +
367E VAL* 3.0 26.2 + - - +
391E GLU* 3.9 23.3 - - + -
395E MET* 5.7 0.4 - - + -
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Residues in contact with PRO 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PRO* 3.8 13.0 - - + -
79B VAL 6.4 0.2 - - - -
80B PRO 4.0 14.8 - - - +
81B SER* 4.0 15.0 - - - +
86B ILE* 4.1 13.6 - - + +
356B ILE* 3.9 8.1 - - + +
357B ARG* 3.4 33.2 - - + +
362E ASP* 3.4 16.4 - - - +
363E TRP* 1.3 95.6 - - + +
365E LEU* 1.3 56.1 + - - +
367E VAL* 3.3 1.6 + - - +
368E LYS* 2.9 30.5 + - - +
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Residues in contact with LEU 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ILE* 4.0 25.8 - - + -
357B ARG* 3.8 9.6 - - - +
354E ALA* 3.5 29.2 - - + -
357E ARG* 3.6 18.6 - - - +
362E ASP* 3.0 28.7 + - + +
364E PRO* 1.3 76.3 - - - +
366E LEU* 1.3 57.1 + - - +
368E LYS* 3.7 2.9 - - + +
369E ASP* 3.0 36.7 + - - +
611E ARG 5.4 1.8 - - - +
612E GLN* 6.1 0.7 - - - -
613E ARG* 4.2 32.5 - - + +
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Residues in contact with LEU 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361E PHE* 3.9 15.7 - - + -
362E ASP 3.1 16.0 + - - +
363E TRP* 3.4 40.8 - - + +
365E LEU* 1.3 78.8 - - - +
367E VAL* 1.3 63.1 + - + +
369E ASP* 3.3 4.1 + - + +
370E PHE* 3.1 50.3 + - + -
391E GLU* 4.3 5.4 - - + -
392E VAL* 3.6 33.0 - - + -
395E MET* 3.8 23.3 - - + -
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Residues in contact with VAL 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.5 31.9 - - + -
76B ASP* 3.9 22.7 - - + +
78B PRO* 3.9 15.5 - - + -
86B ILE* 3.4 23.6 - - + -
363E TRP 3.0 14.9 + - - +
364E PRO 4.0 0.9 - - - +
366E LEU* 1.3 77.1 - - + +
368E LYS* 1.3 64.1 + - - +
370E PHE* 3.3 2.6 + - - +
371E ASN* 2.9 31.9 + - - +
395E MET* 4.3 13.5 - - + -
399E TYR* 4.7 5.8 - - - +
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Residues in contact with LYS 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 3.0 24.2 + - - +
86B ILE* 3.4 20.3 + - - +
87B SER 3.6 6.5 + - - -
88B GLN* 2.8 29.5 + - - +
356B ILE* 3.6 33.5 - - + +
552D ASP 4.3 7.1 + - - -
553D PRO* 5.6 0.6 - - - +
364E PRO 2.9 18.6 + - - +
365E LEU* 3.7 5.6 - - - +
367E VAL* 1.3 76.3 - - - +
369E ASP* 1.3 56.0 - - - +
371E ASN* 3.1 4.3 + - - +
372E LEU* 2.9 33.6 + - + +
613E ARG* 3.9 34.3 + - + -
614E GLN* 4.7 4.8 - - - +
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Residues in contact with ASP 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E LYS* 2.7 37.1 + - - +
365E LEU 3.0 21.5 + - - +
366E LEU* 3.3 6.2 + - + +
368E LYS* 1.3 75.1 - - - +
370E PHE* 1.3 61.8 + - + +
372E LEU* 3.2 3.3 + - - +
373E LEU* 2.8 33.4 + - - +
589E PHE* 3.4 15.1 - - + -
613E ARG* 2.8 46.3 + - - +
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Residues in contact with PHE 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E LYS* 6.2 1.8 - - - -
366E LEU* 3.1 41.0 + - + -
367E VAL 3.9 2.7 - - - +
369E ASP* 1.3 76.6 - - + +
371E ASN* 1.3 67.3 + - - +
373E LEU* 3.6 14.3 - - + +
374E ARG* 3.0 28.7 + - - +
381E PHE* 4.0 9.9 - + - -
392E VAL* 3.7 9.0 - - + -
395E MET* 3.5 42.6 - - + -
396E CYS* 3.7 37.5 - - - -
399E TYR* 4.0 27.6 - + + -
401E ILE* 4.0 21.1 - - + -
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Residues in contact with ASN 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 6.2 0.2 - - - +
76B ASP 5.4 1.6 + - - -
86B ILE* 2.9 40.7 + - - +
87B SER* 3.7 18.4 - - - +
88B GLN* 4.1 9.2 - - + +
367E VAL* 2.9 23.3 + - - +
368E LYS 3.5 8.1 - - - +
370E PHE* 1.3 77.9 - - - +
372E LEU* 1.3 55.6 + - - +
374E ARG* 3.6 6.5 + - - +
375E TRP* 3.0 27.4 + - - +
399E TYR* 4.6 12.5 + - - -
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Residues in contact with LEU 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.3 36.1 - - + +
552D ASP* 5.8 0.2 - - + -
368E LYS* 2.9 19.0 + - - +
369E ASP 3.6 6.5 - - - +
371E ASN* 1.3 73.5 - - - +
373E LEU* 1.3 61.7 + - - +
375E TRP* 3.5 9.8 - - + +
376E LEU* 2.8 32.5 + - - +
589E PHE* 3.9 19.7 - - + -
609E PHE* 3.7 31.8 - - + -
613E ARG* 3.7 46.4 - - + +
615E PRO* 5.7 2.0 - - + -
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Residues in contact with LEU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348E VAL* 3.8 29.6 - - + -
350E LYS* 4.5 8.3 - - - -
369E ASP 2.8 20.2 + - - +
370E PHE* 3.3 27.6 + - + +
372E LEU* 1.3 75.9 - - - +
374E ARG* 1.3 61.1 + - - +
376E LEU* 3.4 4.3 + - + +
377E GLY 3.1 3.5 + - - -
378E ALA* 3.0 45.9 + - + +
380E ALA 5.2 0.4 - - - +
381E PHE* 3.8 32.3 - - + -
401E ILE* 4.3 14.4 - - + -
589E PHE* 3.9 15.7 - - + -
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Residues in contact with ARG 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E TYR* 2.6 73.2 + - + +
297E PRO* 4.7 12.3 - - - +
370E PHE 3.0 19.1 + - - +
371E ASN* 3.9 7.2 - - - +
373E LEU* 1.3 73.6 - - - +
375E TRP* 1.3 65.9 + - - +
377E GLY 3.1 8.3 + - - -
399E TYR* 3.9 34.1 + - + +
401E ILE* 4.8 7.0 - - + -
627E TRP* 3.5 5.4 - - - -
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Residues in contact with TRP 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.7 29.4 + - + -
90B TRP* 6.2 0.4 - - - +
552D ASP* 3.4 24.9 + - + -
371E ASN 3.0 19.1 + - - +
372E LEU* 3.5 11.4 - - + +
374E ARG* 1.3 75.8 - - - +
376E LEU* 1.3 81.1 + - + +
609E PHE* 3.9 28.9 - + - -
615E PRO* 4.4 10.3 - - + -
619E ALA* 4.6 6.3 - - + -
620E PHE* 3.7 38.1 - + - -
623E ARG* 3.0 65.9 + - - +
627E TRP* 3.0 17.4 + - - -
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Residues in contact with LEU 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E VAL* 3.8 22.0 - - + -
372E LEU 2.8 17.4 + - - +
373E LEU* 3.5 9.6 - - + +
375E TRP* 1.3 90.5 - - + +
377E GLY* 1.3 57.8 + - - +
378E ALA* 4.1 9.2 - - + +
589E PHE* 5.0 0.2 - - + -
608E ILE* 3.8 29.6 - - + -
609E PHE* 4.3 11.0 - - + -
619E ALA 3.7 23.1 - - - +
622E LEU* 4.3 8.1 - - + -
623E ARG* 3.4 32.7 - - + +
626E TYR* 3.5 14.9 - - + +
627E TRP* 3.6 2.5 - - - -
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Residues in contact with GLY 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E TYR* 4.2 0.9 - - - -
292E LEU* 3.8 12.6 - - - +
346E HIS* 2.8 32.7 + - - -
373E LEU 3.1 0.6 + - - -
374E ARG 3.1 14.0 + - - -
375E TRP 3.2 1.2 + - - -
376E LEU* 1.3 78.8 - - - +
378E ALA* 1.3 59.9 + - - +
626E TYR* 3.5 6.3 - - - +
627E TRP* 3.5 20.9 - - - -
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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
------------------------------------------------------------
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