Contacts of the helix formed by residues 407 - 417 (chain A) in PDB entry 5I4E
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 GLY 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A CYS* 4.2 1.8 - - - -
406A LEU* 1.3 72.7 - - - +
408A VAL* 1.3 55.3 - - - -
409A THR 3.3 2.9 - - - -
410A ASP* 3.3 16.0 + - - +
411A PHE* 2.9 35.0 + - - +
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Residues in contact with VAL 408 (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 ASN* 5.5 8.1 - - + -
397A ALA* 4.9 8.7 - - + +
398A GLN* 4.2 33.7 - - + +
401A CYS* 3.7 25.8 - - + -
406A LEU 3.8 1.8 + - - +
407A GLY* 1.3 69.9 - - - +
409A THR* 1.4 56.5 + - - +
411A PHE* 3.5 2.4 + - - +
412A SER* 2.7 42.4 + - - +
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Residues in contact with THR 409 (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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407A GLY 3.3 0.6 - - - -
408A VAL* 1.4 75.2 - - - +
410A ASP* 1.4 63.2 + - - +
412A SER* 3.1 6.9 + - - -
413A ARG* 2.8 45.2 + - + +
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Residues in contact with ASP 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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407A GLY* 3.3 17.0 + - - +
409A THR* 1.4 78.8 - - - +
411A PHE* 1.3 56.8 + - - +
413A ARG* 3.9 4.4 - - - +
414A ALA* 2.9 32.2 + - - +
625A LEU* 3.4 28.6 - - + +
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Residues in contact with PHE 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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375A PHE* 4.4 7.0 - + - -
378A ILE* 4.0 12.3 - - + -
391A MET* 4.5 1.8 - - + -
397A ALA* 4.3 10.5 - - + -
400A LEU* 3.7 28.7 - - + -
401A CYS* 3.6 22.0 - - - -
406A LEU* 4.4 17.3 - - + -
407A GLY 2.9 17.4 + - - +
408A VAL 3.5 3.6 - - - +
410A ASP* 1.3 75.6 - - - +
412A SER* 1.3 61.4 + - - +
414A ALA* 3.2 2.6 + - - +
415A LEU* 2.8 61.5 + - + +
440A LEU* 4.1 10.8 - - + -
622A VAL* 3.9 34.1 - - + -
625A LEU* 3.7 9.3 - - + +
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Residues in contact with SER 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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391A MET* 4.2 22.8 - - - +
394A ASN* 6.1 0.5 - - - +
397A ALA* 4.9 1.4 - - - +
408A VAL* 2.7 30.3 + - - +
409A THR* 3.1 6.0 + - - -
411A PHE* 1.3 80.7 - - - +
413A ARG* 1.3 53.4 + - - +
415A LEU* 4.7 2.0 - - - -
416A LEU* 2.8 49.1 + - - +
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Residues in contact with ARG 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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409A THR* 2.8 30.0 + - + +
410A ASP* 4.0 4.5 - - - +
412A SER* 1.3 72.5 - - - +
414A ALA* 1.4 55.2 + - - +
416A LEU* 5.2 0.7 - - - -
417A THR* 2.8 56.2 + - - +
428A GLN* 3.3 30.0 - - - +
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Residues in contact with ALA 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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410A ASP 2.9 19.1 + - - +
411A PHE 3.6 2.5 - - - +
413A ARG* 1.4 77.9 - - - +
415A LEU* 1.3 52.6 + - - +
418A PRO* 3.1 20.9 - - - +
619A ASN* 2.8 22.3 + - - -
621A ASN* 3.5 24.0 - - + +
622A VAL* 3.8 6.5 - - + -
625A LEU* 3.5 21.8 - - + -
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Residues in contact with LEU 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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380A LEU* 4.5 4.9 - - + -
391A MET* 4.4 11.9 - - + -
411A PHE* 2.8 37.3 + - + +
412A SER 3.9 2.2 - - - +
414A ALA* 1.3 74.9 - - - +
416A LEU* 1.3 76.8 + - + +
418A PRO* 3.8 1.0 - - - +
431A GLN* 3.8 15.8 - - - +
436A ALA* 4.0 18.9 - - + +
439A ALA* 4.1 14.8 - - + -
440A LEU* 3.8 46.0 - - + +
443A LEU* 4.4 12.6 - - + -
619A ASN* 4.2 2.5 + - - +
622A VAL* 3.9 8.7 - - + +
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Residues in contact with LEU 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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380A LEU* 3.8 26.5 - - + -
388A GLN* 3.1 27.4 + - - +
389A ALA* 4.0 28.9 - - + +
390A THR* 4.3 1.1 - - - -
391A MET* 4.1 29.4 - - + +
412A SER* 2.8 31.0 + - - +
413A ARG* 5.2 0.2 - - - -
415A LEU* 1.3 87.2 - - + +
417A THR* 1.3 62.0 + - + +
418A PRO* 3.6 1.6 - - - -
431A GLN* 3.4 18.5 + - - +
436A ALA* 4.5 2.7 - - + -
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Residues in contact with THR 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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388A GLN* 4.2 17.9 - - - +
413A ARG* 2.8 40.4 + - - +
416A LEU* 1.3 84.1 - - + +
418A PRO* 1.4 61.6 - - - +
419A ARG 3.5 0.2 + - - -
428A GLN* 2.7 29.8 + - - +
429A LYS 3.1 16.2 - - - +
430A ALA* 4.8 1.8 - - - -
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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