Contacts of the strand formed by residues 340 - 345 (chain H) in PDB entry 2HPC
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 340 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310H LEU* 5.9 0.7 - - + -
329H PHE* 4.3 13.0 - - + -
330H THR 3.6 2.5 - - - -
331H VAL* 4.8 0.4 - - - +
339H GLN* 1.3 74.0 - - - +
341H SER* 1.3 62.9 + - - +
342H VAL* 3.5 27.6 - - + -
353H LEU* 5.2 13.0 - - + -
370H HIS 3.1 26.0 - - - +
371H ASN* 3.6 1.4 - - - +
372H GLY* 2.9 22.3 + - - -
373H MET 2.8 25.2 + - - +
403H TRP* 3.3 53.6 - - + +
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Residues in contact with SER 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H GLY 4.2 0.8 - - - -
329H PHE* 3.3 1.0 - - - -
330H THR* 2.8 51.1 + - - +
332H GLN* 5.2 4.3 + - - +
339H GLN* 4.1 18.7 + - - +
340H ILE* 1.3 73.2 + - - +
342H VAL* 1.3 64.2 + - - +
343H ASN* 5.8 2.5 - - - -
371H ASN* 4.0 6.5 - - - -
372H GLY* 5.9 0.2 - - - -
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Residues in contact with VAL 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H LEU* 4.7 4.0 - - + -
326H TYR* 3.5 30.5 - - + -
328H GLY 2.8 7.4 - - - +
329H PHE* 3.7 17.3 - - + -
340H ILE* 3.5 26.7 - - + -
341H SER* 1.3 82.3 - - - +
343H ASN* 1.3 64.3 + - - +
353H LEU* 4.4 10.1 - - + -
354H MET* 3.5 13.4 - - + +
371H ASN* 2.5 47.2 + - + +
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Residues in contact with ASN 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326H TYR* 3.2 8.1 - - - -
328H GLY* 2.4 67.9 + - - -
341H SER* 5.8 1.6 - - - -
342H VAL* 1.3 72.2 - - - +
344H LYS* 1.3 89.3 + - + +
345H TYR* 3.2 2.9 - - - -
354H MET* 3.8 11.4 - - - -
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Residues in contact with LYS 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H PRO* 5.9 4.4 - - - +
325H HIS 3.5 0.3 - - - +
327H GLY* 3.4 41.4 + - - +
328H GLY* 4.4 1.6 - - - -
343H ASN* 1.3 99.6 + - - +
345H TYR* 1.3 64.9 + - - +
346H ARG* 3.2 17.2 + - - +
354H MET* 4.1 3.6 - - - +
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Residues in contact with TYR 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324H ALA* 3.4 20.4 - - + -
325H HIS 3.0 9.2 - - - -
326H TYR* 3.5 25.1 - + + +
343H ASN 3.2 2.0 - - - -
344H LYS* 1.3 74.8 - - - +
346H ARG* 1.3 81.7 + - - +
347H GLY 3.2 16.8 + - - -
350H GLY* 2.7 30.4 + - - -
351H ASN* 2.8 58.1 + - + +
354H MET* 3.1 12.9 - - + +
355H ASP* 5.0 3.1 - - - -
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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