Contacts of the strand formed by residues 249 - 254 (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 TRP 249 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H CYS* 4.0 0.9 - - - -
240H CYS* 3.2 4.2 - - - -
241H ASP* 2.6 60.8 + - + +
244H THR* 3.0 20.5 + - + -
245H GLU* 2.6 38.6 + - + +
247H GLY 4.0 3.8 - - - -
248H GLY* 1.3 73.2 - - - +
250H THR* 1.3 59.4 + - - +
251H VAL 3.3 4.0 + - - -
309H GLU* 4.1 1.1 - - + -
311H LEU* 3.9 11.2 - - + +
325H HIS* 2.7 41.3 - + - -
453H LYS* 3.2 39.9 - - + -
454H ILE* 3.3 17.9 - - - -
455H ARG* 2.9 54.2 - - + +
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Residues in contact with THR 250 (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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210H GLU* 4.3 6.8 + - - +
211H CYS* 3.0 33.6 + - - +
227H ILE* 3.7 17.0 - - + +
238H VAL* 3.3 26.0 - - + -
248H GLY 3.6 1.4 + - - -
249H TRP* 1.3 70.1 - - - +
251H VAL* 1.3 60.6 + - - +
252H ILE* 2.6 40.2 - - + +
294H LEU* 4.3 2.0 - - + -
302H LEU* 4.0 10.5 - - + -
454H ILE* 2.9 22.1 + - - -
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Residues in contact with VAL 251 (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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239H TYR* 2.8 40.6 + - + +
240H CYS 5.1 1.1 - - - -
241H ASP* 5.2 1.8 - - + +
249H TRP 3.3 3.9 + - - +
250H THR* 1.3 75.9 - - - +
252H ILE* 1.3 65.2 + - - +
253H GLN 3.6 18.6 - - - +
254H ASN* 4.3 7.0 - - + -
289H PRO* 5.5 4.5 - - + -
292H TYR* 2.8 45.6 + - + +
294H LEU* 3.4 10.7 - - - +
451H SER* 5.3 5.2 - - - -
453H LYS* 3.8 24.2 - - + -
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Residues in contact with ILE 252 (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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250H THR* 2.6 33.9 - - + +
251H VAL* 1.3 79.5 - - - +
253H GLN* 1.3 61.5 + - + +
292H TYR* 4.6 0.4 - - - -
293H TRP* 3.6 9.2 - - + -
294H LEU* 3.1 34.5 + - + +
299H ILE* 3.2 44.4 - - + -
302H LEU* 5.0 3.8 - - + -
329H PHE* 5.7 2.0 - - + -
452H MET* 2.7 30.0 + - + +
454H ILE* 3.5 37.9 - - + +
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Residues in contact with GLN 253 (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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251H VAL* 3.6 6.9 - - - +
252H ILE* 1.3 74.2 - - - +
254H ASN* 1.3 68.2 + - - +
255H ARG* 3.1 27.4 - - - +
262H PHE* 4.2 3.6 - - + -
292H TYR 3.1 12.6 - - - +
293H TRP* 3.2 20.9 - - + -
412H PRO* 4.1 4.6 - - - +
413H ASN* 3.1 33.2 + - - +
450H MET* 2.9 22.5 + - - +
451H SER* 3.2 4.7 - - - -
452H MET* 3.0 59.2 + - - +
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Residues in contact with ASN 254 (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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251H VAL* 4.3 12.8 - - + -
253H GLN* 1.3 79.5 - - - +
255H ARG* 1.3 75.9 + - - +
256H GLN* 2.6 40.1 + - - +
262H PHE* 4.0 1.2 - - - -
289H PRO* 3.6 21.6 - - - +
290H GLY 4.2 4.9 - - - +
291H GLU* 3.2 25.6 - - - +
292H TYR* 3.1 12.1 + - + +
449H LYS* 4.0 10.9 + - - -
450H MET 4.0 3.1 - - - -
451H SER* 3.0 22.2 + - - -
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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