Contacts of the helix formed by residues 455 - 460 (chain K) in PDB entry 2I2X
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 455 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135K PHE* 4.6 36.6 - - + -
136K LEU 5.2 0.2 - - - +
170K GLU* 4.8 1.0 + - - -
452K LYS 4.0 20.7 + - - -
453K VAL 3.4 9.2 + - - +
454K PHE* 1.3 81.9 + - - +
456K PRO* 1.3 65.4 - - + +
457K GLU* 3.3 24.9 - - + +
458K ASN* 3.0 45.2 + - - +
459K TYR* 4.0 3.8 - - - -
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Residues in contact with PRO 456 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444K LEU* 3.6 28.3 - - + -
448K LYS* 3.9 26.9 - - + +
454K PHE* 3.5 23.8 - - + +
455K LYS* 1.3 82.6 - - + +
457K GLU* 1.3 66.2 + - - +
458K ASN 3.1 0.2 - - - -
459K TYR* 2.9 21.2 + - + +
461K PHE* 3.0 39.8 + - + +
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Residues in contact with GLU 457 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ARG* 3.8 12.9 - - - +
455K LYS* 3.4 25.0 - - + +
456K PRO* 1.3 84.1 - - - +
458K ASN* 1.3 60.8 + - - +
459K TYR 2.9 10.1 + - - -
460K GLY* 3.0 12.0 + - - -
461K PHE* 3.6 17.1 + - - +
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Residues in contact with ASN 458 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K LEU* 3.1 27.6 + - - +
137K GLN* 3.3 6.9 - - - -
138K LEU* 2.7 53.5 + - + +
139K ARG* 3.3 20.1 + - - -
170K GLU* 4.8 3.2 + - - -
195K ASP* 4.8 1.6 - - - +
453K VAL 5.4 0.8 + - - -
455K LYS* 3.0 37.2 + - - +
457K GLU* 1.3 79.3 - - - +
459K TYR* 1.3 76.4 + - + +
460K GLY 3.6 0.4 - - - -
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Residues in contact with TYR 459 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136K LEU* 3.7 6.6 - - - +
138K LEU* 3.6 21.0 - - + +
139K ARG* 3.6 12.4 + - - +
167K GLY* 4.2 1.6 - - - -
168K GLY 2.9 24.4 + - - -
170K GLU* 2.5 31.4 + - - -
191K LEU* 3.7 48.7 - - + -
194K ILE* 3.7 16.2 - - + +
195K ASP* 4.5 7.2 - - + -
454K PHE* 3.6 20.0 - + - -
455K LYS 4.0 4.9 - - - -
456K PRO* 2.9 10.3 + - + +
458K ASN* 1.3 90.7 - - + +
460K GLY* 1.3 62.6 + - - +
461K PHE* 3.3 30.7 - - + -
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Residues in contact with GLY 460 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ARG* 3.6 18.8 - - - -
457K GLU* 3.0 12.6 + - - -
458K ASN 3.6 0.2 - - - -
459K TYR* 1.3 79.0 - - - +
461K PHE* 1.3 65.8 + - - +
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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