Contacts of the helix formed by residues 391 - 403 (chain A) in PDB entry 3ZRH
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 PRO 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A ASP 3.8 2.9 - - - +
390A LEU* 1.3 93.3 - - + +
392A PRO* 1.3 75.7 - - + +
393A THR* 3.2 5.8 - - + -
394A VAL* 2.9 23.2 + - + +
395A GLN* 2.9 19.8 + - - +
687A TYR 5.8 0.2 - - - +
690A ILE 5.3 3.4 - - - +
691A ARG* 6.1 3.6 - - - +
692A PRO 4.1 20.0 - - - +
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Residues in contact with PRO 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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390A LEU 3.5 4.9 - - - +
391A PRO* 1.3 84.7 - - + +
393A THR* 1.3 63.2 + - + +
395A GLN* 3.2 13.9 + - + +
396A GLU* 3.1 22.5 + - - +
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Residues in contact with THR 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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391A PRO* 4.3 7.2 - - + -
392A PRO* 1.3 76.3 - - + +
394A VAL* 1.3 62.9 + - + +
396A GLU* 3.5 8.2 + - - +
397A LYS* 3.1 26.9 + - - +
692A PRO* 4.0 22.9 - - + +
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Residues in contact with VAL 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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390A LEU* 3.9 20.2 - - + -
391A PRO* 2.9 29.5 + - + +
393A THR* 1.3 78.4 - - + +
395A GLN* 1.3 66.4 + - - +
397A LYS* 3.2 7.2 + - + +
398A LEU* 2.9 20.8 + - - +
687A TYR* 3.7 36.2 - - + +
690A ILE* 3.8 32.3 - - + +
692A PRO 4.1 10.1 - - - +
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Residues in contact with GLN 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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387A ILE* 3.4 26.1 + - + +
388A GLU* 3.4 23.6 + - - +
390A LEU* 3.1 28.4 + - + -
391A PRO 2.9 10.9 + - - +
392A PRO* 3.2 15.7 + - + +
394A VAL* 1.3 77.0 - - - +
396A GLU* 1.3 57.2 + - - +
398A LEU* 3.0 8.1 + - - +
399A PHE* 2.8 51.3 + - + -
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Residues in contact with GLU 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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392A PRO 3.1 13.2 + - - +
393A THR* 3.5 7.8 + - - +
394A VAL 3.3 0.2 - - - -
395A GLN* 1.3 78.3 - - - +
397A LYS* 1.3 57.8 + - - +
399A PHE* 4.4 3.8 - - - +
400A ASP* 2.8 45.7 + - - +
405A ARG* 3.7 21.6 + - - +
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Residues in contact with LYS 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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393A THR 3.1 18.8 + - - +
394A VAL* 3.6 6.5 - - + +
396A GLU* 1.3 79.9 - - - +
398A LEU* 1.3 62.1 + - - +
400A ASP* 3.4 9.3 + - - +
401A GLU* 2.9 57.7 + - - +
686A ARG* 3.6 24.4 - - - +
687A TYR* 4.2 3.8 - - + -
690A ILE* 3.8 30.7 - - + -
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Residues in contact with LEU 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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387A ILE* 4.1 19.7 - - + -
390A LEU* 4.0 17.5 - - + -
394A VAL 2.9 14.2 + - - +
395A GLN* 3.5 9.0 - - - +
397A LYS* 1.3 76.2 - - - +
399A PHE* 1.3 90.6 + - + +
401A GLU* 3.1 3.3 + - - +
402A VAL* 3.0 24.6 + - + +
683A TRP* 3.7 35.0 - - + -
684A LEU* 4.3 4.9 - - + -
687A TYR* 3.6 40.4 + - + -
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Residues in contact with PHE 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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383A LEU* 4.4 13.5 - - + -
387A ILE* 4.0 17.0 - - + -
395A GLN* 2.8 39.6 + - + +
396A GLU* 3.9 4.9 - - - +
398A LEU* 1.3 88.8 - - + +
400A ASP* 1.3 65.6 + - - +
402A VAL* 4.4 0.9 - - + -
403A LEU* 2.9 52.0 + - + +
405A ARG* 3.9 23.0 + - - +
433A TYR* 4.2 24.7 - + - -
592A MET* 3.8 24.0 - - + -
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Residues in contact with ASP 400 (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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340A ALA 3.9 3.6 - - - +
341A LYS* 3.0 27.7 + - - -
396A GLU* 2.8 41.2 + - - +
397A LYS* 3.6 9.7 - - - +
398A LEU 3.4 0.2 - - - -
399A PHE* 1.3 73.4 - - - +
401A GLU* 1.3 60.8 + - + +
403A LEU 3.8 0.9 - - - +
405A ARG* 2.7 39.3 + - - +
1694A EDO 4.4 2.0 + - - -
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Residues in contact with GLU 401 (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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339A ALA 4.9 6.1 - - - +
340A ALA 3.5 23.3 - - - +
341A LYS* 3.7 11.1 - - - +
342A CYS* 2.9 37.0 + - - +
343A ILE* 3.8 1.0 - - - +
397A LYS* 2.9 44.7 + - - +
398A LEU 3.1 2.7 + - - +
399A PHE 3.0 0.6 - - - -
400A ASP* 1.3 81.9 - - + +
402A VAL* 1.3 58.6 + - - +
686A ARG* 2.7 22.6 + - - -
687A TYR* 2.6 36.3 + - - +
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Residues in contact with VAL 402 (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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342A CYS 4.4 0.7 - - - +
343A ILE* 4.0 11.2 - - + +
344A PRO* 4.0 20.4 - - + -
383A LEU* 4.8 9.6 - - + -
398A LEU* 3.0 32.3 + - + +
399A PHE* 4.7 0.9 - - + -
401A GLU* 1.3 79.0 - - - +
403A LEU* 1.3 82.8 + - + +
435A LEU* 3.7 17.4 - - + +
436A TRP* 3.0 25.3 + - - +
683A TRP* 3.9 24.9 - - + -
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Residues in contact with LEU 403 (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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341A LYS* 3.1 26.3 + - - -
383A LEU* 4.8 2.2 - - + -
399A PHE* 2.9 50.2 + - + +
400A ASP 3.8 2.1 - - - +
402A VAL* 1.3 95.5 - - + +
404A ASP* 1.3 65.8 + - - +
405A ARG* 3.6 18.4 + - - +
408A GLN* 4.6 13.7 - - + +
433A TYR* 3.9 35.0 - - + -
434A ALA 3.4 12.8 - - - +
435A LEU* 4.3 7.9 - - + -
436A TRP* 3.6 2.5 - - - -
1694A EDO 3.6 0.7 + - - -
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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