Contacts of the helix formed by residues 435 - 439 (chain B) in PDB entry 3H1I
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 PHE 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B GLU* 3.2 17.5 - - - +
245B ARG* 3.6 35.4 - - - +
424B MET* 4.4 0.7 - - - -
433B THR 4.5 4.5 - - - -
434B PRO* 1.3 77.4 - - + +
436B LEU* 1.3 67.5 + - - +
437B ASP* 3.8 13.5 - - - +
438B GLU* 2.8 48.2 + - + +
439B LEU* 4.1 4.2 - - - +
168O TYR 4.2 1.3 - - - -
169O LYS* 3.6 56.3 - - + -
170O THR* 6.1 0.4 - - + -
240O TRP* 3.9 28.5 - + - -
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Residues in contact with LEU 436 (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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241B GLY 5.0 5.8 - - - +
242B GLY 5.7 0.2 - - - +
243B GLU* 3.0 35.2 + - + +
257B VAL* 4.4 9.6 - - + -
421B LYS* 5.8 2.7 - - + -
422B LYS* 2.9 56.6 - - + +
423B SER* 4.1 2.2 - - - +
424B MET* 3.7 31.8 - - + +
435B PHE* 1.3 69.7 - - - +
437B ASP* 1.3 56.2 + - + +
438B GLU 3.1 5.0 + - - -
439B LEU* 3.5 24.7 + - + +
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Residues in contact with ASP 437 (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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243B GLU* 4.0 2.8 + - - +
435B PHE* 2.8 9.3 + - - +
436B LEU* 1.3 78.1 - - + +
438B GLU* 1.3 60.2 + - - +
439B LEU 3.6 1.3 - - - +
169O LYS* 3.1 23.9 + - - -
240O TRP* 3.8 26.8 + - - +
421O LYS* 4.7 16.5 + - - +
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Residues in contact with GLU 438 (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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338B ARG* 4.8 10.5 - - - +
433B THR 4.6 0.3 - - - +
434B PRO* 3.3 18.0 - - + +
435B PHE* 2.8 53.4 + - + +
437B ASP* 1.3 79.5 - - - +
439B LEU* 1.3 70.9 + - - +
169O LYS* 3.9 21.7 + - - +
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Residues in contact with LEU 439 (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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257B VAL* 4.4 25.8 - - + -
337B ILE* 5.0 6.5 - - + -
338B ARG* 4.2 29.2 - - + +
341B MET* 4.0 43.9 - - + +
345B LYS* 6.2 1.8 - - - -
422B LYS* 4.1 13.3 + - + +
424B MET* 5.2 4.5 - - + -
434B PRO* 4.2 18.2 - - + -
435B PHE 4.1 4.5 - - - +
436B LEU* 3.5 27.2 + - + +
437B ASP* 3.6 0.8 - - - -
438B GLU* 1.3 90.3 - - - +
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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