Contacts of the helix formed by residues 478 - 484 (chain B) in PDB entry 4X2Q
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 GLY 478 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ILE* 5.7 10.5 - - - -
131B TYR* 3.7 27.3 - - - -
132B TYR* 3.7 24.5 + - - -
135B TRP* 4.3 1.4 + - - -
479B GLU* 1.3 65.9 + - - +
480B PHE* 3.3 2.7 - - - -
481B GLY* 3.1 18.9 + - - +
482B LEU* 4.0 2.9 + - - +
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Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A MET* 3.9 39.7 - - + +
144A ILE* 5.8 4.1 - - + +
131B TYR* 3.8 5.2 + - - +
135B TRP* 3.6 41.4 - - + +
478B GLY* 1.3 71.5 - - - +
480B PHE* 1.3 65.5 + - + +
481B GLY 3.1 1.6 + - - -
482B LEU* 3.5 25.7 + - - +
483B ARG* 3.9 26.0 + - - +
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Residues in contact with PHE 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A HIS 5.5 0.2 - - - -
141A GLY* 5.1 0.4 - - - -
142A MET* 3.8 28.7 - - + -
144A ILE* 5.8 2.2 - - + -
154A THR* 3.4 37.2 - - + -
156A HIS* 3.5 31.0 - + - -
488A VAL* 3.8 30.7 - - + -
490A THR* 5.5 2.2 - - + -
478B GLY* 3.3 1.0 - - - -
479B GLU* 1.3 75.7 - - + +
481B GLY* 1.3 61.6 + - - +
482B LEU 3.4 0.2 - - - -
483B ARG* 3.6 59.3 + - - +
484B GLU* 4.6 3.3 + - - +
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Residues in contact with GLY 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR* 4.2 11.4 - - - -
181B PRO* 4.6 3.9 - - - +
478B GLY 3.1 17.0 + - - +
479B GLU 3.1 2.2 - - - -
480B PHE* 1.3 78.9 - - - +
482B LEU* 1.3 59.2 + - - +
483B ARG 3.3 0.7 - - - -
484B GLU* 3.5 26.1 - - - +
485B TYR* 4.1 5.5 - - - -
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B TYR* 4.3 12.5 - - + -
135B TRP* 3.5 52.0 - - + +
139B ILE* 4.1 29.4 - - + -
156B HIS* 6.1 0.4 - - - +
181B PRO* 4.7 8.1 - - - +
184B CYS* 4.2 9.0 - - - -
185B CYS* 3.5 21.5 - - - -
478B GLY 4.0 1.9 + - - +
479B GLU* 3.6 21.5 - - - +
480B PHE 3.4 0.2 - - - -
481B GLY* 1.3 73.0 - - - +
483B ARG* 1.3 67.7 + - + +
484B GLU 3.2 2.5 - - - -
485B TYR* 3.4 10.2 + - - +
486B SER* 3.3 14.9 + - - +
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A MET* 4.4 6.7 - - - +
156A HIS* 4.7 6.7 - - - -
483A ARG* 3.3 58.2 - - - +
156B HIS* 6.3 3.6 - - + -
479B GLU* 3.9 34.5 + - - +
480B PHE* 3.6 52.3 - - - +
481B GLY 3.3 1.2 - - - -
482B LEU* 1.3 82.6 - - + +
484B GLU* 1.3 57.4 + - - +
486B SER* 3.3 24.0 + - - +
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Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ILE* 3.3 17.3 - - - +
178B LYS* 5.9 0.5 - - - -
240B LYS* 3.6 14.9 + - - +
242B ALA* 4.4 2.3 - - - +
264B ARG* 5.0 1.6 + - - -
266B THR* 3.3 43.9 + - + +
480B PHE 4.6 3.2 + - - +
481B GLY* 3.5 19.4 + - - +
483B ARG* 1.3 77.6 - - - +
485B TYR* 1.3 85.7 + - + +
486B SER 3.5 1.6 - - - -
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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