Contacts of the helix formed by residues 469 - 477 (chain A) in PDB entry 5I4V
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 LYS 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ILE* 6.4 0.9 - - + -
455A GLU* 3.1 11.2 + - - -
466A GLY 3.3 22.5 + - - +
467A SER* 4.3 9.6 - - - +
468A HIS* 1.3 80.6 - - - +
470A ILE* 1.3 63.2 + - - +
471A LEU 3.3 2.2 - - - -
472A HIS* 3.3 28.5 + - + +
473A ARG* 3.1 22.3 + - - +
240E LYS* 6.3 3.4 - - - +
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Residues in contact with ILE 470 (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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451A PRO* 3.4 46.2 - - + +
452A LEU* 3.6 25.4 - - + +
455A GLU* 2.9 21.9 + - + +
463A SER* 5.5 0.2 - - - -
468A HIS* 3.7 21.8 - - + +
469A LYS* 1.3 75.1 - - - +
471A LEU* 1.3 61.3 + - - +
473A ARG* 3.3 8.4 + - + +
474A LEU* 3.0 32.8 + - + +
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Residues in contact with LEU 471 (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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279A VAL* 5.0 8.1 - - + -
283A VAL* 3.6 31.0 - - + -
301A ILE* 4.1 37.9 - - + +
304A LEU* 4.3 16.6 - - + -
305A LYS* 4.4 12.3 - - + +
452A LEU* 4.6 6.9 - - + +
455A GLU* 2.9 17.9 + - + +
456A ILE* 4.9 12.6 - - + -
470A ILE* 1.3 75.7 - - - +
472A HIS* 1.3 66.7 + - - +
474A LEU* 3.1 14.0 + - + +
475A LEU* 2.9 33.3 + - + +
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Residues in contact with HIS 472 (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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297A ARG* 3.2 43.2 - - + +
301A ILE* 4.3 19.0 - - + +
469A LYS* 3.3 36.4 + - + +
471A LEU* 1.3 78.9 - - - +
473A ARG* 1.3 51.7 + - - +
475A LEU* 3.2 6.1 + - - +
476A GLN* 2.8 54.5 + - - +
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Residues in contact with ARG 473 (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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469A LYS 3.1 10.2 + - - +
470A ILE* 3.4 12.6 - - + +
471A LEU 3.1 0.2 - - - -
472A HIS* 1.3 79.5 - - - +
474A LEU* 1.3 63.7 + - + +
476A GLN* 3.0 43.5 + - - +
477A ASP* 3.2 10.5 + - - +
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Residues in contact with LEU 474 (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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279A VAL* 4.9 1.3 - - + -
280A GLN* 4.1 32.1 - - + +
283A VAL* 4.0 23.1 - - + +
284A ASP* 5.6 0.3 - - - +
287A LYS* 3.1 22.2 + - - -
452A LEU* 4.1 33.2 - - + -
470A ILE* 3.0 22.1 + - + +
471A LEU* 3.1 15.5 + - + +
473A ARG* 1.3 77.7 - - + +
475A LEU* 1.3 56.9 + - - +
477A ASP* 3.9 8.1 + - - +
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Residues in contact with LEU 475 (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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283A VAL* 4.3 12.3 - - + -
287A LYS* 3.2 35.3 + - + +
292A PHE* 3.9 19.7 - - + -
293A LEU* 5.4 0.7 - - + -
297A ARG* 4.0 25.9 + - + +
300A GLN* 3.6 32.1 - - + +
301A ILE* 3.9 27.6 - - + +
304A LEU* 4.4 8.1 - - + -
471A LEU* 2.9 22.8 + - + +
472A HIS* 3.4 7.4 - - - +
474A LEU* 1.3 76.3 - - - +
476A GLN* 1.3 66.6 + - - +
477A ASP 3.1 2.1 + - - -
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Residues in contact with GLN 476 (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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297A ARG* 3.1 28.4 + - - +
472A HIS* 2.8 46.7 + - - +
473A ARG* 3.1 37.0 - - - +
475A LEU* 1.3 72.4 - - - +
477A ASP* 1.3 60.3 + - - +
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Residues in contact with ASP 477 (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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284A ASP* 5.8 0.3 - - - +
287A LYS* 3.3 22.2 + - - +
473A ARG* 3.2 10.1 + - - +
474A LEU* 4.0 12.8 - - - +
475A LEU 3.1 1.9 + - - -
476A GLN* 1.3 83.5 - - - +
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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