Contacts of the helix formed by residues 389 - 400 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A ARG* 3.4 28.7 - - + +
352A GLU* 2.8 19.1 + - - +
361A PHE* 3.7 25.1 - - + -
388A TYR* 1.3 74.8 - - - +
390A GLU* 1.3 66.1 + - - +
391A GLU* 3.7 14.4 - - - +
392A VAL* 3.0 23.8 + - + +
393A MET* 3.6 3.8 + - - +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.7 34.0 - - + -
122A ARG* 4.1 10.7 + - - -
124A GLY* 4.7 7.1 - - - +
148A PRO* 3.6 28.6 - - - +
216A ARG* 4.4 9.2 + - - +
388A TYR 3.4 1.7 + - - -
389A ALA* 1.3 74.5 - - - +
391A GLU* 1.3 69.5 + - - +
393A MET* 2.9 20.1 + - - +
394A GLN* 2.9 19.3 + - - +
436A ARG* 3.7 38.7 + - + +
437A ASP* 5.1 1.8 - - - +
440A HIS* 4.7 5.0 - - - +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.2 28.6 + - + +
216A ARG* 5.6 0.9 - - - +
217A SER* 4.7 15.4 + - - -
361A PHE* 3.6 47.6 - - + -
363A TRP* 3.9 24.0 + - + -
366A LEU* 4.5 1.8 - - + -
389A ALA* 3.7 6.8 - - - +
390A GLU* 1.3 88.8 + - - +
392A VAL* 1.3 62.1 + - - +
394A GLN* 3.4 14.0 + - - +
395A MET* 3.0 28.3 + - - +
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LYS* 6.2 0.4 - - + -
352A GLU* 4.3 4.9 - - + +
361A PHE* 4.7 4.5 - - + -
366A LEU* 3.7 22.7 - - + -
370A PHE* 4.1 10.8 - - + -
381A PHE* 3.8 27.6 - - + -
388A TYR* 4.1 22.0 - - + -
389A ALA* 3.0 28.2 + - + +
391A GLU* 1.3 76.4 - - - +
393A MET* 1.3 64.5 + - + +
395A MET* 3.2 4.6 + - - +
396A CYS* 3.0 26.3 + - - -
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Residues in contact with MET 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A PHE* 4.3 1.8 - - + -
383A THR* 3.8 25.6 - - + -
388A TYR* 4.4 6.1 - - + +
389A ALA 3.6 5.1 + - - +
390A GLU* 2.9 8.1 + - - +
392A VAL* 1.3 92.9 - - + +
394A GLN* 1.3 65.6 + - - +
396A CYS* 3.2 7.8 + - - +
397A ASP* 3.0 27.2 + - - +
403A VAL* 4.1 29.6 - - + -
405A ASP* 4.3 2.9 - - - +
436A ARG* 4.1 12.1 - - - +
437A ASP* 4.0 22.7 - - - +
440A HIS* 3.4 26.9 - - + +
442A ALA* 4.8 0.6 - - - +
443A VAL* 4.3 11.9 - - - -
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Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 2.8 55.9 - - - +
323A PRO* 6.6 0.4 - - + -
363A TRP* 5.9 1.6 - - - -
390A GLU* 2.9 21.9 + - - +
391A GLU* 3.5 14.8 - - - +
393A MET* 1.3 76.3 - - - +
395A MET* 1.3 62.3 + - + +
397A ASP* 3.4 8.5 + - - +
398A ARG* 3.2 31.8 + - - +
440A HIS* 4.2 15.6 - - + -
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Residues in contact with MET 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TRP* 5.2 0.4 - - + -
366A LEU* 3.8 28.0 - - + +
367A VAL* 4.3 10.5 - - + -
370A PHE* 3.5 44.4 - - + -
391A GLU 3.0 16.5 + - - +
392A VAL 3.2 8.0 + - - +
394A GLN* 1.3 74.8 - - + +
396A CYS* 1.3 60.2 + - - +
398A ARG* 3.0 16.6 + - - +
399A TYR* 2.8 63.6 + - + +
44D LEU* 4.0 17.0 - - + -
76D ASP* 4.0 3.6 - - - +
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Residues in contact with CYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TRP* 3.8 0.2 - - - -
370A PHE* 3.6 10.1 - - - -
381A PHE* 3.3 38.6 - - - -
392A VAL 3.0 21.3 + - - -
393A MET* 3.2 10.5 + - - +
395A MET* 1.3 74.4 - - - +
397A ASP* 1.3 62.4 + - - +
400A GLY* 2.9 21.3 + - - -
401A ILE 3.2 25.6 + - - +
403A VAL* 3.5 16.2 - - + -
442A ALA* 3.6 12.7 - - + +
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Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TRP* 2.9 26.2 + - - +
298A ALA* 3.5 5.9 - - - +
300A LEU* 3.8 16.7 - - + +
323A PRO* 5.4 6.9 - - + +
393A MET 3.0 9.8 + - - +
394A GLN* 3.5 10.4 - - - +
395A MET 3.3 0.2 - - - -
396A CYS* 1.3 77.0 - - - +
398A ARG* 1.3 60.3 + - + +
439A ASN 4.9 0.2 - - - +
440A HIS* 2.6 33.8 + - - +
441A PRO* 3.2 23.6 - - + +
442A ALA* 3.0 31.2 + - - +
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Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ALA* 3.4 14.1 - - - +
300A LEU* 3.7 22.4 - - + -
394A GLN* 3.2 20.8 + - - +
395A MET* 3.0 18.0 + - - +
397A ASP* 1.3 77.5 - - + +
399A TYR* 1.3 75.2 + - + +
400A GLY 3.5 0.2 - - - -
44D LEU* 3.9 10.3 - - - +
76D ASP* 2.9 42.4 + - - -
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A TYR* 3.6 19.8 - - - +
297A PRO* 4.9 3.6 - - - +
298A ALA* 4.0 4.0 - - - +
367A VAL* 4.7 6.4 - - - +
370A PHE* 4.0 25.1 - + + -
371A ASN* 4.6 12.7 + - - -
374A ARG* 3.6 32.9 + - - +
395A MET* 2.8 46.4 + - + +
398A ARG* 1.3 90.0 - - + +
400A GLY* 1.3 62.1 + - - +
401A ILE* 4.1 17.9 - - + +
76D ASP* 2.6 41.5 + - - +
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Residues in contact with GLY 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A TRP* 3.6 20.9 - - - -
290A PRO* 3.4 9.4 - - - +
291A TYR* 2.8 30.8 + - - +
297A PRO* 5.1 0.2 - - - -
298A ALA* 3.5 10.9 - - - +
379A ASN 3.9 1.9 - - - +
396A CYS 2.9 8.6 + - - -
398A ARG 3.5 2.4 - - - -
399A TYR* 1.3 78.7 - - - +
401A ILE* 1.3 61.9 + - - +
402A VAL 3.5 3.0 + - - -
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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