Contacts of the helix formed by residues 462 - 470 (chain A) in PDB entry 4IYM
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 HIS 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A VAL* 4.1 25.1 - - + -
109A PHE* 5.1 1.1 - - + -
156A TRP* 3.8 43.6 + + - +
441A VAL* 5.7 0.4 - - - +
442A PRO 3.8 12.7 + - - -
443A LEU 3.2 23.3 - - - -
444A ALA* 3.0 14.1 + - - +
446A HIS 2.7 22.3 + - - -
447A SER* 3.7 14.8 - - - -
448A PHE* 3.5 17.5 - - + +
461A GLN* 1.3 93.8 + - + +
463A GLY* 1.3 69.7 + - - +
465A ASP* 3.7 0.5 + - - +
466A SER* 3.1 31.8 + - - -
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Residues in contact with GLY 463 (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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109A PHE* 3.4 24.6 - - - -
444A ALA 3.1 11.6 + - - -
445A TYR 3.9 4.3 - - - -
446A HIS 3.1 22.3 + - - -
447A SER* 4.3 1.6 - - - -
462A HIS* 1.3 81.1 - - - +
464A THR* 1.3 60.2 + - - -
466A SER* 2.8 19.9 + - - -
467A ILE* 3.8 2.6 + - - +
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Residues in contact with THR 464 (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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109A PHE* 4.1 0.9 - - + -
116A LEU* 4.2 12.1 - - + -
135A ARG* 5.0 2.9 + - - -
445A TYR 4.7 1.4 + - - -
447A SER* 5.2 1.0 - - - -
463A GLY* 1.3 71.3 - - - -
465A ASP* 1.3 69.7 + - - +
467A ILE* 3.2 20.7 + - + +
468A LYS* 3.2 12.3 + - - +
120B GLU* 4.4 17.3 + - - +
468B LYS* 5.4 2.4 + - - -
115C HIS* 3.6 32.5 - - + +
118C LYS* 4.7 1.8 - - - +
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Residues in contact with ASP 465 (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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447A SER* 4.2 8.7 + - - -
458A ASP 4.5 0.9 - - - +
459A LEU* 3.6 16.5 - - + +
460A ASN* 2.7 51.6 + - + +
462A HIS 3.9 4.7 - - - +
463A GLY* 3.2 0.6 - - - -
464A THR* 1.3 81.2 + - - +
466A SER* 1.3 57.5 + - - +
468A LYS* 3.1 8.0 + - - +
469A PHE* 2.9 26.7 + - - +
468B LYS* 2.8 38.3 + - - -
473B THR* 4.6 4.4 + - - -
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Residues in contact with SER 466 (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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109A PHE* 4.5 2.1 - - - -
160A PRO* 3.3 28.0 - - - +
243A GLN* 5.6 2.0 - - - +
460A ASN 3.8 6.2 + - - -
461A GLN* 5.0 0.4 - - - -
462A HIS* 3.1 35.5 + - - -
463A GLY 2.8 17.5 + - - -
465A ASP* 1.3 77.0 - - - +
467A ILE* 1.3 63.8 + - - +
469A PHE* 3.2 5.3 + - - +
470A TRP* 3.1 35.3 + - - +
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Residues in contact with ILE 467 (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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109A PHE* 4.5 4.0 - - + -
110A VAL* 5.0 2.9 - - + -
113A ILE* 4.1 18.8 - - + -
116A LEU* 3.8 41.7 - - + +
117A GLN* 4.4 7.4 - - + -
135A ARG* 3.6 19.3 - - - +
160A PRO* 4.3 13.9 - - + -
164A CYS* 4.0 17.0 - - - -
463A GLY 3.9 11.9 - - - +
464A THR* 3.2 12.7 + - - +
466A SER* 1.3 85.1 + - - +
468A LYS* 1.3 56.1 + - - +
470A TRP 3.5 0.7 + - - -
471A THR* 2.6 38.2 + - + +
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Residues in contact with LYS 468 (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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135A ARG* 4.2 28.7 - - - +
241A ARG* 3.4 4.0 + - - -
459A LEU* 4.0 14.8 - - + +
464A THR 3.2 8.0 + - - +
465A ASP* 3.1 12.1 + - - +
467A ILE* 1.3 79.8 - - - +
469A PHE* 1.3 57.8 + - - +
471A THR* 3.0 30.5 + - - +
473A THR* 4.0 17.3 + - - -
458B ASP 4.6 5.3 - - - +
459B LEU* 4.0 18.4 - - + -
464B THR* 5.1 4.6 + - - -
465B ASP* 2.8 36.8 + - - -
468B LYS* 5.7 3.1 - - + -
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Residues in contact with PHE 469 (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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138A VAL* 4.2 1.6 - - - +
218A ALA* 3.8 22.2 - - + -
219A VAL 3.4 23.3 - - - -
220A SER* 4.7 0.2 - - - -
241A ARG* 2.7 45.0 + - + +
242A ALA 3.6 22.9 - - - -
243A GLN* 3.7 34.8 - - + +
459A LEU* 3.7 11.4 - - + -
465A ASP 2.9 12.7 + - - +
466A SER* 3.2 10.0 + - - +
468A LYS* 1.3 76.9 - - - +
470A TRP* 1.3 89.5 + + - +
471A THR 3.3 0.2 - - - -
458B ASP* 3.3 26.7 - - - -
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Residues in contact with TRP 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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137A PRO* 4.2 0.3 - - - +
138A VAL* 3.7 20.5 + - + -
141A GLY* 3.5 28.0 - - - -
142A ALA 4.1 9.2 - - - -
157A MSE 3.7 15.1 + - + +
160A PRO* 3.9 11.9 - - + +
161A ALA* 3.4 33.0 - - + -
164A CYS* 3.8 9.1 - - - +
166A ASN* 2.9 33.6 + - - +
168A PHE* 3.4 28.7 - + - -
218A ALA* 3.8 15.3 - - + -
220A SER* 4.1 13.2 - - - -
243A GLN* 4.8 4.6 + - - -
466A SER* 3.1 27.2 + - - +
468A LYS 3.3 0.4 - - - -
469A PHE* 1.3 102.3 - + - +
471A THR* 1.3 63.2 + - - +
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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