Contacts of the helix formed by residues 409 - 420 (chain A) in PDB entry 2HRC
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 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A VAL 3.3 11.0 - - - +
408A ASN* 1.3 90.5 - - - +
410A VAL* 1.3 58.5 + - - +
411A CYS 3.4 0.3 + - - -
412A ARG* 3.6 12.6 + - + +
413A GLU* 3.4 23.9 + - - +
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Residues in contact with VAL 410 (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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97A ASP* 3.6 10.3 - - - +
204A ASN* 3.8 21.3 - - - +
207A TYR* 3.8 12.3 - - + -
208A ARG* 3.0 38.8 - - + +
408A ASN* 3.0 34.9 + - - +
409A PRO* 1.3 77.1 - - - +
411A CYS* 1.3 64.8 + - - +
413A GLU* 3.1 9.4 + - - +
414A THR* 2.8 44.1 + - - +
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Residues in contact with CYS 411 (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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196A CYS* 5.5 2.9 - - - -
204A ASN* 4.4 12.6 - - - -
402A SER* 4.4 5.2 + - - +
406A CYS* 3.6 8.7 - - - -
408A ASN* 3.2 25.2 + - - +
410A VAL* 1.3 86.9 - - - +
412A ARG* 1.3 58.4 + - - +
414A THR* 3.4 2.8 + - - -
415A LYS* 3.0 27.5 + - - +
1501A FES 2.4 49.4 - - - -
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Residues in contact with ARG 412 (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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402A SER* 4.5 7.8 + - - +
408A ASN 4.5 0.6 + - - +
409A PRO* 3.6 9.6 + - + +
410A VAL 3.3 0.8 - - - -
411A CYS* 1.3 78.9 - - - +
413A GLU* 1.3 78.3 + - - +
415A LYS* 3.3 25.2 + - - +
416A SER* 3.0 52.0 + - - -
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Residues in contact with GLU 413 (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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207A TYR* 3.3 44.8 + - + +
208A ARG* 4.4 3.5 + - - -
409A PRO* 3.4 17.3 - - - +
410A VAL* 3.1 21.8 + - - +
412A ARG* 1.3 97.3 + - - +
414A THR* 1.3 56.8 + - - +
416A SER* 3.5 6.7 + - - -
417A PHE* 2.9 27.4 + - - +
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Residues in contact with THR 414 (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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203A LEU* 3.5 45.8 - - + +
204A ASN* 2.7 30.8 + - - +
207A TYR* 3.8 13.4 - - + +
399A LEU* 6.0 1.3 - - + -
410A VAL* 2.8 20.4 + - - +
411A CYS* 3.7 4.3 - - - -
413A GLU* 1.3 74.0 - - - +
415A LYS* 1.3 67.5 + - - +
417A PHE* 3.2 15.7 + - - +
418A PHE* 3.3 15.8 + - + -
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Residues in contact with LYS 415 (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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399A LEU* 3.4 34.9 - - + +
400A THR* 3.5 34.3 + - - +
402A SER* 4.5 12.6 + - - +
411A CYS 3.0 14.3 + - - +
412A ARG* 3.5 32.2 - - - +
414A THR* 1.3 77.5 - - - +
416A SER* 1.3 65.4 + - - +
418A PHE* 3.2 5.2 + - - +
419A THR* 2.9 40.8 + - + +
827B ARG* 4.7 7.3 - - - +
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Residues in contact with SER 416 (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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412A ARG* 3.0 34.6 + - - -
413A GLU* 3.8 5.8 - - - -
415A LYS* 1.3 81.9 - - - +
417A PHE* 1.3 66.5 + - - +
419A THR* 3.5 10.4 + - - -
420A SER* 2.7 35.2 + - - -
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Residues in contact with PHE 417 (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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206A ILE* 3.9 19.1 - - + -
207A TYR* 4.0 29.2 - + + -
210A TYR* 3.7 39.0 - + + -
217A PRO* 3.8 17.5 - - + -
221A TRP* 4.2 7.6 - + - -
413A GLU 2.9 15.5 + - - +
414A THR* 3.2 11.6 + - - +
416A SER* 1.3 78.7 - - - +
418A PHE* 1.3 86.8 + + - +
420A SER* 4.3 1.7 - - - -
421A GLN* 2.8 49.8 + - - +
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Residues in contact with PHE 418 (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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187A ALA* 4.1 3.8 - - + -
203A LEU* 3.9 39.3 - - + -
206A ILE* 4.1 15.7 - - + -
221A TRP* 4.3 10.5 - + + +
222A SER* 4.0 21.5 - - - -
223A THR* 3.7 35.7 - - + -
394A LEU* 3.5 21.4 - - - +
395A CYS* 4.7 5.6 - - + -
399A LEU* 4.7 9.0 - - + -
414A THR* 3.3 28.0 + - + -
415A LYS 3.2 5.6 + - - +
417A PHE* 1.3 103.0 - + - +
419A THR* 1.3 65.6 + - - +
420A SER 3.1 2.6 + - - -
421A GLN* 3.4 15.0 + - - +
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Residues in contact with THR 419 (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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394A LEU* 3.4 20.6 - - - +
395A CYS* 3.8 23.3 - - - -
400A THR* 4.1 17.9 - - + -
415A LYS* 2.9 35.0 + - + +
416A SER* 3.5 11.3 + - - -
418A PHE* 1.3 75.1 - - - +
420A SER* 1.3 63.3 + - - +
421A GLN 3.4 0.2 - - - -
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Residues in contact with SER 420 (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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416A SER* 2.7 29.4 + - - -
417A PHE* 4.3 2.5 - - - -
419A THR* 1.3 80.9 + - - +
421A GLN* 1.3 65.7 + - - +
422A GLN* 3.5 1.6 + - - -
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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