Contacts of the strand formed by residues 401 - 405 (chain X) in PDB entry 3I39
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 THR 401 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243X GLU* 3.1 11.4 - - - +
244X SER* 2.8 45.1 + - - -
245X ASN* 6.0 0.9 - - + +
399X ILE* 6.3 1.1 - - + -
400X LYS* 1.3 77.6 - - - +
402X LYS* 1.3 62.2 + - - +
403X VAL* 4.2 1.0 - - - +
482X MET 2.7 23.1 + - - -
483X ARG* 3.5 21.4 - - - +
484X HIS 4.5 1.1 - - - -
485X GLY* 3.9 19.1 - - - +
488X ASP* 5.9 1.1 - - - -
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Residues in contact with LYS 402 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241X VAL* 4.1 23.3 - - + +
242X THR 3.6 9.6 - - - +
243X GLU* 4.5 5.2 - - + +
401X THR* 1.3 78.4 - - - +
403X VAL* 1.3 68.1 + - - +
404X VAL* 4.1 16.6 - - + -
482X MET 4.8 1.2 - - - +
485X GLY* 5.3 0.3 - - - -
487X MET* 3.9 0.7 + - - +
488X ASP* 3.5 54.4 + - - +
489X PRO* 4.3 6.8 - - - +
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Residues in contact with VAL 403 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240X VAL 3.8 0.3 - - - +
241X VAL* 3.4 2.6 - - - -
242X THR* 2.8 55.1 + - + +
243X GLU 4.0 0.7 - - - +
244X SER* 3.6 40.4 - - - +
301X LEU* 4.6 2.7 - - + -
401X THR* 4.2 1.6 - - - +
402X LYS* 1.3 80.0 - - - +
404X VAL* 1.3 71.7 + - - +
405X ALA* 4.0 13.0 - - + -
482X MET* 3.7 26.9 - - + +
487X MET* 3.7 17.3 - - + -
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Residues in contact with VAL 404 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239X PRO* 5.2 3.6 - - + -
240X VAL 3.3 11.7 - - - +
241X VAL* 4.2 15.5 - - + -
402X LYS* 4.1 14.8 - - - -
403X VAL* 1.3 73.2 - - - +
405X ALA* 1.3 67.6 + - - +
407X PHE* 4.0 23.3 - - + -
487X MET* 2.8 32.1 + - - +
489X PRO* 3.7 27.8 - - + -
513X LEU* 6.5 0.7 - - + -
518X PRO* 4.0 20.4 - - + +
520X VAL 4.8 0.2 - - - +
522X HIS* 4.6 0.9 - - - +
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Residues in contact with ALA 405 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239X PRO* 3.2 8.0 - - - +
240X VAL* 2.9 31.7 + - + -
301X LEU* 3.4 31.4 - - + -
302X MET* 4.4 0.2 - - - -
403X VAL* 4.0 6.2 - - + +
404X VAL* 1.3 75.3 - - - +
406X GLY* 1.3 62.4 + - - +
407X PHE* 3.5 13.1 + - - -
522X HIS* 3.7 25.6 - - + -
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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