Contacts of the strand formed by residues 301 - 305 (chain H) in PDB entry 2HU4
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 PRO 301 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274H HIS 3.2 24.7 - - - +
275H TYR* 4.1 17.7 - - + -
290H VAL* 3.8 0.9 - - - -
291H CYS* 2.9 38.7 + - - +
292H ARG 4.1 6.7 - - - +
293H ASP 3.9 10.8 - - - +
299H ASN 3.7 7.4 - - - +
300H ARG* 1.3 86.1 - - - +
302H TRP* 1.3 59.9 + - - +
315H GLY 3.4 7.4 - - - +
316H TYR* 3.4 33.6 - - + +
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Residues in contact with TRP 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H TYR* 2.9 18.5 + - - -
288H THR* 5.5 0.9 - - + -
289H CYS 3.1 15.3 - - - +
290H VAL* 4.4 3.8 - - + -
300H ARG 4.9 0.2 - - - +
301H PRO* 1.3 75.5 - - - +
303H VAL* 1.3 70.2 + - - +
304H SER* 3.4 20.0 - - - -
313H GLN* 3.2 34.5 - - + -
314H ILE* 3.5 21.2 - - - -
315H GLY* 2.7 45.0 + - - -
316H TYR* 3.3 21.6 + - - +
317H ILE* 3.7 7.6 - - + -
383H TRP* 3.3 53.7 - + + +
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Residues in contact with VAL 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240H VAL* 5.8 4.7 - - + -
254H ILE* 4.0 9.2 - - + -
268H LEU* 3.7 28.5 - - + -
275H TYR* 2.9 40.8 - - + +
278H CYS* 5.2 1.8 - - - -
287H ILE 3.8 0.9 - - - +
288H THR* 3.6 1.1 - - - -
289H CYS* 2.8 43.3 + - + +
291H CYS* 4.9 3.8 - - - -
302H TRP* 1.3 75.6 - - - +
304H SER* 1.3 64.6 + - - +
305H PHE* 3.9 19.8 - - + -
312H TYR* 4.3 1.8 - - + -
313H GLN 3.3 11.7 - - - +
314H ILE* 4.1 2.0 - - + -
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Residues in contact with SER 304 (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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286H GLU* 5.4 4.5 - - - -
287H ILE 3.1 11.9 - - - -
288H THR* 4.1 15.0 - - - -
302H TRP* 3.4 20.8 - - - -
303H VAL* 1.3 73.7 - - - +
305H PHE* 1.3 62.9 + - - +
312H TYR* 3.1 3.8 - - - +
313H GLN* 2.7 47.3 + - - +
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Residues in contact with PHE 305 (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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238H PHE* 3.9 25.6 - + + -
239H THR 5.5 0.4 - - - -
240H VAL* 4.8 4.3 - - + -
254H ILE* 3.6 48.2 - - + -
280H CYS* 5.3 0.7 - - - -
286H GLU* 3.6 13.4 + - - +
287H ILE* 3.1 56.6 + - + +
289H CYS* 3.9 24.5 - - - -
303H VAL* 3.9 9.0 - - + -
304H SER* 1.3 82.2 - - - +
306H ASN* 1.3 71.2 + - - +
310H LEU* 4.3 7.4 - - + -
311H GLU 3.0 19.5 - - - +
312H TYR* 3.5 9.6 - - + -
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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
------------------------------------------------------------
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