Contacts of the helix formed by residues 329 - 333 (chain A) in PDB entry 4IF8
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 SER 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLU* 2.8 17.8 + - - -
320A LYS 6.1 0.2 - - - -
324A SER* 6.1 2.2 - - - -
327A GLY 5.1 1.8 + - - -
328A VAL* 1.4 75.3 - - - +
330A LYS* 1.4 59.3 + - - +
331A ILE 3.2 2.7 - - - -
332A PHE* 2.9 36.7 + - - +
333A GLU* 3.5 21.5 + - - +
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Residues in contact with LYS 330 (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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93A SER* 3.4 41.6 + - - +
94A THR* 3.5 20.7 + - - +
97A GLU* 2.8 37.4 + - - +
329A SER* 1.4 71.9 + - - +
331A ILE* 1.4 55.0 + - - +
333A GLU* 2.9 40.6 + - - +
335A HIS* 3.4 27.8 - - + +
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Residues in contact with ILE 331 (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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83A PHE* 4.1 7.4 - - + -
86A LEU* 3.9 26.0 - - + -
90A ALA* 5.1 0.4 - - + -
94A THR* 3.6 19.2 - - + +
97A GLU* 4.5 1.0 + - - -
98A ILE* 4.1 15.2 - - + +
328A VAL* 4.0 20.4 - - + -
329A SER 4.5 0.2 - - - -
330A LYS* 1.4 76.7 - - - +
332A PHE* 1.3 87.0 + - + +
333A GLU 3.3 2.2 + - - +
338A LEU* 3.7 31.2 - - + +
348A LYS* 3.9 3.5 - - - -
349A VAL* 2.9 47.4 + - + +
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Residues in contact with PHE 332 (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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83A PHE* 3.9 20.0 - + - -
319A LEU 3.9 9.6 - - - -
320A LYS* 3.6 60.8 + - + -
323A LEU* 4.3 3.8 - - + -
328A VAL 4.0 11.9 - - - -
329A SER* 2.9 19.8 + - - +
331A ILE* 1.3 96.3 - - + +
333A GLU* 1.3 62.4 + - + +
348A LYS* 3.4 22.4 + - - +
349A VAL* 3.4 29.1 - - + +
351A GLU 5.3 0.2 - - - -
352A ALA* 3.8 24.7 - - + -
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Residues in contact with GLU 333 (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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94A THR* 5.2 0.2 + - - -
329A SER* 3.5 26.9 + - - +
330A LYS* 2.9 24.6 + - - +
331A ILE 4.2 1.0 - - - +
332A PHE* 1.3 81.3 - - - +
334A GLU* 1.3 63.3 + - - +
335A HIS* 2.7 41.6 + - + +
338A LEU* 5.5 1.2 - - - +
347A LEU 4.2 1.4 - - - +
348A LYS* 3.3 18.7 - - - +
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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