Contacts of the helix formed by residues 430 - 434 (chain B) in PDB entry 7V3X
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 ILE 430 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B LEU* 4.5 11.2 - - + -
380B LEU* 3.9 28.3 - - + -
392B PHE* 4.5 14.8 - - + -
393B ARG* 4.8 12.3 - - + -
396B VAL* 4.3 26.5 - - + -
414B ASN* 5.4 2.7 - - - +
426B THR* 3.3 26.0 + - + +
428B SER* 3.9 23.1 - - - +
429B HIS* 1.3 73.6 - - - +
431B SEP 1.3 63.1 + - - +
432B THR* 3.2 4.0 - - - -
433B ILE* 3.1 23.0 + - + +
434B THR* 3.6 13.2 + - + +
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Residues in contact with SEP 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 3.9 32.9 + - - +
415A THR* 5.3 2.1 - - - +
416A SER 4.6 9.2 + - - -
417A ASP* 4.1 16.3 + - - -
419A PHE* 5.3 3.3 + - - +
285B LEU* 5.0 3.1 - - - -
425B ILE* 3.8 23.1 + - - +
426B THR* 2.7 45.4 + - - -
429B HIS* 3.5 20.8 + - - +
430B ILE* 1.3 75.1 + - - +
432B THR* 1.3 67.2 + - - +
434B THR* 2.7 30.4 + - - +
437B ILE* 4.1 9.0 - - - -
457B LYS* 3.4 8.1 + - - -
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Residues in contact with THR 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 4.8 1.6 - - - +
318A GLU* 3.4 37.5 - - - +
381A SER* 5.0 4.5 - - - +
382A ALA* 5.8 1.9 - - - +
385A ARG* 3.6 21.5 + - - -
415A THR* 3.9 32.8 - - + +
429B HIS 4.7 6.2 + - - +
430B ILE* 4.6 3.1 - - - -
431B SEP 1.3 84.4 + - - +
433B ILE* 1.3 59.6 + - - +
457B LYS* 4.5 1.6 - - - +
459B ARG* 2.8 29.4 + - - +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 5.3 5.6 - - - +
385A ARG* 5.3 4.3 - - - +
283B ILE* 4.6 2.6 - - - +
396B VAL* 4.8 9.2 - - + -
397B ILE* 4.5 21.5 - - + -
400B THR* 3.8 25.7 - - + +
404B LYS* 5.5 4.7 + - - +
430B ILE* 3.1 21.4 + - + +
432B THR* 1.3 82.3 + - - +
434B THR* 1.3 60.4 + - + +
435B ASP* 4.4 5.4 - - - +
459B ARG* 4.7 1.1 + - - -
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 4.0 22.2 - - + -
284B ILE 5.0 0.2 - - - +
285B LEU* 3.4 38.1 - - + -
380B LEU* 6.2 1.1 - - + -
412B PHE* 6.3 0.7 - - + -
430B ILE* 3.8 15.5 - - + +
431B SEP 2.7 21.0 + - - +
433B ILE* 1.3 79.0 - - + +
435B ASP* 1.3 60.2 + - - +
436B THR 4.0 4.9 - - - -
437B ILE* 3.6 18.2 - - - +
457B LYS* 3.3 7.5 + - - -
459B ARG* 3.1 22.5 + - - -
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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