Contacts of the strand formed by residues 402 - 406 (chain X) in PDB entry 4HSC
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 ASN 402 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391X ALA 3.7 0.5 - - - +
392X VAL* 3.0 8.9 - - - +
393X VAL* 2.9 50.8 + - + +
400X GLU 3.6 3.8 + - - +
401X HIS* 1.3 76.7 + - - +
403X LYS* 1.3 74.3 + - - +
404X VAL* 3.8 17.7 - - - +
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Residues in contact with LYS 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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276X GLY 5.4 1.4 + - - -
277X THR* 3.1 26.9 + - - +
278X LEU 3.8 14.6 + - - -
279X GLY* 4.9 1.4 - - - +
390X THR* 3.8 24.7 - - + -
391X ALA 3.5 2.5 - - - -
392X VAL* 4.1 5.6 - - + -
402X ASN* 1.3 83.6 + - - +
404X VAL* 1.3 70.2 + - - +
405X VAL* 4.2 14.8 - - + -
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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
----------------------------------------------------------
389X PHE 3.8 0.5 - - - +
390X THR* 3.1 5.3 - - - +
391X ALA* 2.8 49.0 + - + +
393X VAL* 6.5 0.7 - - + -
402X ASN* 3.8 17.3 - - - +
403X LYS* 1.3 79.8 - - - +
405X VAL* 1.3 73.0 + - - +
406X THR* 4.3 4.2 + - + -
411X VAL* 4.4 22.4 - - + -
412X ILE* 4.8 1.5 - - + +
415X VAL* 4.9 14.1 - - + -
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Residues in contact with VAL 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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388X SER* 3.7 17.3 - - - +
389X PHE 3.2 9.6 - - - +
390X THR* 3.8 20.9 - - + +
403X LYS* 4.2 17.0 - - + -
404X VAL* 1.3 80.5 - - - +
406X THR* 1.3 66.9 + - - +
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Residues in contact with THR 406 (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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388X SER* 3.8 2.7 + - - -
389X PHE* 2.8 34.0 + - + +
404X VAL* 4.7 4.3 - - + -
405X VAL* 1.3 77.7 - - - +
407X LYS* 1.3 62.6 + - - +
408X ASP* 3.0 34.4 + - - +
411X VAL* 3.9 20.6 - - + +
412X ILE* 3.5 31.0 - - + -
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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