Contacts of the helix formed by residues 389 - 400 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216B ARG* 3.3 28.5 - - + +
352B GLU* 2.8 18.5 + - - +
361B PHE* 3.8 23.1 - - + -
388B TYR* 1.3 75.9 - - - +
390B GLU* 1.3 66.8 + - - +
391B GLU* 3.6 15.7 - - - +
392B VAL* 3.0 23.1 + - + +
393B MET* 3.6 4.2 + - - +
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.7 34.8 - - + -
122B ARG* 4.0 11.6 + - - -
124B GLY* 4.7 7.9 - - - +
148B PRO* 3.6 26.6 - - - +
216B ARG* 4.5 9.0 - - - +
388B TYR 3.5 1.7 + - - -
389B ALA* 1.3 75.7 - - - +
391B GLU* 1.3 67.8 + - - +
393B MET* 3.0 12.1 + - - +
394B GLN* 2.9 28.7 + - - +
436B ARG* 3.7 39.3 + - + +
437B ASP* 5.1 0.9 - - - +
440B HIS* 4.7 5.3 - - - +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 3.4 30.3 + - + +
216B ARG* 5.7 1.0 - - - +
217B SER* 4.9 13.5 + - - -
361B PHE* 3.6 38.9 - - + -
363B TRP* 3.8 27.9 - - + -
366B LEU* 4.5 2.7 - - + -
389B ALA* 3.1 14.9 - - - +
390B GLU* 1.3 82.9 + - - +
392B VAL* 1.3 56.1 + - - +
394B GLN* 3.4 14.5 + - - +
395B MET* 3.1 32.6 + - - +
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Residues in contact with VAL 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B LYS* 6.3 0.7 - - + -
352B GLU* 4.2 11.7 - - + +
361B PHE* 4.8 5.2 - - + -
366B LEU* 3.8 22.7 - - + -
370B PHE* 4.2 10.3 - - + -
381B PHE* 3.8 19.3 - - + -
388B TYR* 4.1 15.3 - - + -
389B ALA* 3.0 27.3 + - + +
391B GLU* 1.3 74.1 - - - +
393B MET* 1.3 79.1 - - + +
395B MET* 3.3 3.9 + - - +
396B CYS* 3.0 26.2 + - - -
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Residues in contact with MET 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PHE* 4.4 1.3 - - + -
383B THR* 4.0 21.5 - - + -
388B TYR* 4.5 6.3 - - + -
389B ALA 3.6 3.3 + - - +
390B GLU* 3.0 8.1 + - - +
392B VAL* 1.3 95.8 - - + +
394B GLN* 1.3 63.9 + - - +
396B CYS* 3.2 16.3 + - - +
397B ASP* 3.0 25.8 + - - +
403B VAL* 4.1 22.4 - - + -
405B ASP* 4.3 8.3 - - - +
436B ARG* 4.1 12.1 - - - +
437B ASP* 4.0 23.3 - - - +
440B HIS* 3.4 30.1 - - + +
442B ALA* 4.8 0.6 - - - +
443B VAL* 4.3 7.6 - - - -
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Residues in contact with GLN 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TYR* 3.0 55.4 - - - +
323B PRO* 6.4 2.2 - - + -
390B GLU* 2.9 21.6 + - - +
391B GLU* 3.6 14.5 - - - +
392B VAL 3.3 0.2 - - - -
393B MET* 1.3 76.2 - - - +
395B MET* 1.3 61.6 + - + +
397B ASP* 3.3 8.1 + - - +
398B ARG* 3.3 31.4 + - - +
440B HIS* 4.0 17.1 - - + -
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Residues in contact with MET 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B TRP* 5.4 0.4 - - + -
366B LEU* 3.8 27.6 - - + -
367B VAL* 4.3 13.5 - - + -
370B PHE* 3.6 35.2 - - + -
391B GLU 3.1 19.5 + - - +
392B VAL 3.6 7.2 - - - +
393B MET 3.2 0.2 - - - -
394B GLN* 1.3 73.2 - - + +
396B CYS* 1.3 61.4 + - - +
398B ARG* 3.1 17.6 + - - +
399B TYR* 2.8 72.8 + - + +
44E LEU* 3.9 15.5 - - + -
76E ASP* 3.9 3.8 - - - +
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Residues in contact with CYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B TRP* 4.0 0.2 - - - -
370B PHE* 3.7 9.4 - - - -
381B PHE* 3.4 29.2 - - - -
392B VAL 3.0 25.4 + - - -
393B MET* 3.4 10.5 - - - +
395B MET* 1.3 77.2 - - - +
397B ASP* 1.3 58.1 + - - +
400B GLY* 2.9 28.2 + - - -
401B ILE* 3.2 24.1 + - - +
403B VAL* 3.4 25.1 - - + -
442B ALA* 3.6 12.1 - - + +
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Residues in contact with ASP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 2.9 25.8 + - - +
298B ALA* 3.4 6.6 - - - +
300B LEU* 3.7 19.2 - - + +
323B PRO* 5.3 7.9 - - + +
393B MET 3.0 9.4 + - - +
394B GLN* 3.5 10.0 - - - +
395B MET 3.3 0.2 - - - -
396B CYS* 1.3 75.4 - - - +
398B ARG* 1.3 60.1 + - + +
439B ASN 4.9 0.2 - - - +
440B HIS* 2.7 34.5 + - - +
441B PRO* 3.3 22.2 - - + +
442B ALA* 3.0 33.6 + - - +
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Residues in contact with ARG 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ALA* 3.3 14.4 - - - +
300B LEU* 3.7 22.2 - - + -
394B GLN* 3.4 18.6 - - - +
395B MET* 3.1 18.3 + - - +
397B ASP* 1.3 77.4 - - + +
399B TYR* 1.3 66.8 + - + +
400B GLY 3.6 0.2 - - - -
44E LEU* 3.7 16.6 - - - +
76E ASP* 2.8 42.6 + - - -
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Residues in contact with TYR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B TYR* 3.5 21.0 - - - +
297B PRO* 5.1 3.3 - - - +
298B ALA* 4.0 3.6 - - - -
367B VAL* 4.7 5.6 - - - +
370B PHE* 3.9 25.4 - + + -
371B ASN* 4.6 12.3 + - - -
374B ARG* 3.6 42.3 + - + +
395B MET* 2.8 52.9 + - + +
398B ARG* 1.3 90.0 - - + +
400B GLY* 1.3 60.1 + - - +
401B ILE* 4.1 17.6 - - + +
76E ASP* 2.6 43.1 + - - +
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Residues in contact with GLY 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 3.7 20.4 - - - -
290B PRO* 3.4 9.7 - - - +
291B TYR* 2.7 30.7 + - - +
298B ALA* 3.5 13.8 - - - +
379B ASN 3.9 1.7 - - - +
396B CYS 2.9 8.7 + - - -
399B TYR* 1.3 77.9 - - - +
401B ILE* 1.3 61.9 + - - +
402B VAL 3.6 2.1 + - - -
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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