Contacts of the helix formed by residues 431 - 435 (chain C) in PDB entry 5X22
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 431 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C ASP* 2.6 33.4 + - - -
326C ASP* 3.1 33.0 - - + +
327C HIS* 3.5 13.0 + + - -
429C ASP* 3.6 4.1 + - - +
430C VAL* 1.3 75.1 - - - +
432C ARG* 1.3 100.0 + - + +
433C THR* 3.0 17.5 + - + +
434C HIS* 3.0 45.9 + - + +
1048D PRO* 5.1 2.7 - - - -
1071D PHE* 3.4 8.1 - - - -
1075D HIS* 4.0 1.1 - - - -
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Residues in contact with ARG 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ASP* 5.8 0.2 + - - -
327C HIS* 3.4 20.7 - - - -
430C VAL 4.0 0.8 + - - -
431C HIS* 1.3 93.1 + - + +
433C THR* 1.3 64.9 + - - +
434C HIS 3.2 0.6 + - - -
435C TYR* 3.5 20.1 - - - +
491C GLU* 4.7 6.1 + - - +
492C ASP* 2.7 40.4 + - - -
516C ARG* 5.0 2.1 + - - -
518C LYS* 3.1 45.8 + - - +
519C GLY* 4.2 14.3 - - - +
1048D PRO* 5.5 1.0 - - - +
1071D PHE* 4.0 14.1 - - + -
1075D HIS* 4.0 9.8 - - + +
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Residues in contact with THR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C HIS* 3.4 40.8 - - + +
328C LEU* 2.9 45.3 + - - +
431C HIS* 3.5 17.3 + - - +
432C ARG* 1.3 89.6 - - + +
434C HIS* 1.3 56.8 + - - +
435C TYR 3.0 6.1 - - - -
437C ARG* 3.1 24.3 + - - +
488C ALA* 3.9 8.5 - - + -
491C GLU* 5.3 3.8 - - - +
492C ASP* 4.6 1.8 - - - +
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Residues in contact with HIS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ASP* 4.6 4.9 - - + -
328C LEU* 3.5 31.8 - - + +
331C ARG* 4.7 11.9 + - - -
427C VAL 5.8 0.2 + - - -
429C ASP 3.7 9.8 + - - -
430C VAL* 4.0 17.7 - - + -
431C HIS* 3.0 46.0 + - + +
433C THR* 1.3 77.0 - - - +
435C TYR* 1.3 63.1 + - - +
436C GLY 3.2 0.5 + - - -
437C ARG 2.9 1.8 + - - -
438C ILE* 2.8 65.8 + - + +
439C CYS 5.5 3.1 - - - -
440C PRO 5.7 0.4 - - - -
453C THR* 6.1 1.5 - - + +
1071D PHE* 4.2 6.1 - - + -
1078D ARG* 5.7 3.8 - - - -
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Residues in contact with TYR 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ARG 3.5 16.9 + - - +
433C THR 3.0 1.2 - - - -
434C HIS* 1.3 76.9 - - - +
436C GLY* 1.3 61.4 + - - +
437C ARG* 3.0 28.6 + - - -
469C THR* 4.2 2.3 - - - +
471C TYR* 4.1 5.8 - - - -
491C GLU* 4.3 2.6 - - - +
498C GLN* 3.2 17.3 + - - -
516C ARG* 3.2 48.5 - - - +
533C ASP* 2.3 34.3 + - - -
538C GLN* 4.4 7.2 - - - -
539C VAL* 3.5 32.8 - - + +
1067D VAL* 4.3 6.4 - - + +
1068D LEU* 4.9 3.1 - - + -
1071D PHE* 3.6 41.9 - + + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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