Contacts of the helix formed by residues 401 - 409 (chain A) in PDB entry 2IVF
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 VAL 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A ASP* 3.4 26.2 - - - +
331A LEU* 3.4 20.8 + - + +
333A LEU 3.0 7.7 + - - +
335A VAL* 3.7 11.8 - - + +
342A PHE* 3.7 19.5 - - + -
399A ARG 3.8 0.2 + - - -
400A THR* 1.3 70.7 - - - +
402A PHE* 1.3 52.7 + - - +
404A GLY* 3.0 4.7 + - - -
405A LEU* 2.8 32.5 + - + +
815A TYR* 3.6 35.4 - - + +
828A LEU* 3.8 17.9 - - + +
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Residues in contact with PHE 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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315A ILE* 3.8 39.3 - - + -
320A PHE* 3.6 30.5 - + - -
325A VAL* 5.1 0.2 - - + -
331A LEU* 2.9 43.2 + - + +
382A LEU* 3.8 31.9 - - + -
383A GLU* 3.8 17.3 - - - -
400A THR* 3.5 5.2 - - - +
401A VAL* 1.3 77.1 - - - +
403A GLU* 1.3 52.7 + - - +
405A LEU* 3.2 8.3 + - + +
406A ARG* 2.8 58.6 + - + +
467A LEU* 4.2 9.2 - - + -
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Residues in contact with GLU 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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382A LEU 4.1 1.1 - - - +
383A GLU* 3.6 2.9 - - - -
384A GLY* 3.0 44.7 + - - +
385A THR* 4.0 8.3 + - - +
399A ARG* 3.7 20.3 + - + +
400A THR* 2.9 22.3 + - - +
402A PHE* 1.3 72.5 - - - +
404A GLY* 1.3 65.1 - - - +
406A ARG* 3.1 34.4 + - - +
407A GLU* 3.3 19.1 + - - +
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Residues in contact with GLY 404 (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 ARG* 3.6 28.4 + - - +
400A THR 3.2 7.6 + - - -
401A VAL* 3.0 8.1 + - - -
403A GLU* 1.3 73.3 - - - +
405A LEU* 1.3 65.7 + - - +
407A GLU* 3.1 7.0 + - - +
408A HIS* 2.9 22.0 + - - +
828A LEU* 4.1 9.6 - - - +
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Residues in contact with LEU 405 (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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308A LEU* 5.2 0.4 - - + -
315A ILE* 4.1 18.6 - - + -
331A LEU* 4.4 16.8 - - + -
401A VAL* 2.8 16.1 + - + +
402A PHE* 3.4 10.8 - - - +
404A GLY* 1.3 74.7 - - - +
406A ARG* 1.3 53.4 + - - +
408A HIS* 4.0 17.7 - - + -
409A LEU* 2.8 51.2 + - + +
463A LEU* 3.7 45.5 - - + -
814A PHE* 6.2 0.4 - - + -
828A LEU* 3.9 23.6 - - + +
829A PRO* 5.0 1.3 - - + -
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Residues in contact with ARG 406 (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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315A ILE* 4.2 19.4 - - + +
318A LYS* 6.2 1.8 - - - +
383A GLU* 3.7 23.1 + - - +
384A GLY 4.9 0.2 - - - +
402A PHE* 2.8 46.7 + - + +
403A GLU* 3.1 39.8 + - - +
405A LEU* 1.3 73.6 - - - +
407A GLU* 1.3 64.0 + - - +
409A LEU* 3.6 8.2 + - - +
410A LYS* 3.5 23.7 + - - +
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Residues in contact with GLU 407 (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 ARG* 3.3 32.9 + - - +
403A GLU 3.3 8.1 + - - +
404A GLY* 3.1 10.2 + - - +
406A ARG* 1.3 80.4 - - - +
408A HIS* 1.3 64.0 + - - +
410A LYS* 3.0 36.4 + - + +
411A ASP* 4.5 1.9 + - - +
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Residues in contact with HIS 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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308A LEU* 4.5 0.4 - - + +
404A GLY 2.9 16.1 + - - +
405A LEU* 3.5 16.8 - - + +
407A GLU* 1.3 79.2 - - - +
409A LEU* 1.3 65.7 + - + +
410A LYS 3.1 1.4 + - - -
411A ASP* 3.2 22.0 + - - +
412A TYR* 3.6 27.8 - + - -
828A LEU* 3.8 26.8 - - + +
829A PRO 2.7 27.6 + - - -
830A THR* 3.4 24.1 + - - -
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Residues in contact with LEU 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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308A LEU* 3.5 51.8 - - + +
311A SER* 4.1 5.8 - - - -
312A GLN* 3.3 41.5 - - + +
315A ILE* 3.6 32.3 - - + -
405A LEU* 2.8 34.6 + - + +
406A ARG* 4.1 6.5 - - - +
407A GLU 3.2 0.4 - - - -
408A HIS* 1.3 74.4 - - + +
410A LYS* 1.3 56.2 + - - +
411A ASP 3.0 5.4 - - - -
412A TYR* 2.9 25.4 + - + -
413A THR* 3.4 0.5 + - - +
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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