Contacts of the strand formed by residues 353 - 356 (chain A) in PDB entry 2HTQ
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 GLY 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A SER 5.0 0.5 - - - +
281A TYR* 3.1 15.1 + - - -
290A VAL* 3.1 32.0 - - - +
317A LEU* 5.5 1.1 - - - -
352A PHE* 1.3 82.7 - - - +
354A PHE* 1.3 65.2 + - - -
360A VAL* 4.5 6.5 - - - -
361A TRP 3.1 12.3 - - - -
362A MET* 4.3 2.9 - - - -
383A TRP* 4.7 0.4 - - - -
409A SER* 5.4 0.2 + - - -
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Residues in contact with PHE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.5 4.7 - - + -
97A PHE* 4.5 10.3 - + + -
281A TYR* 3.5 36.3 - + + -
352A PHE* 3.2 41.5 - + - -
353A GLY* 1.3 73.1 - - - -
355A ARG* 1.3 64.9 + - - +
356A GLN* 3.9 6.6 - - + +
360A VAL* 3.0 9.6 - - - +
361A TRP* 2.7 48.6 + - + +
383A TRP* 3.9 0.9 - - - -
409A SER* 3.6 10.3 - - - -
410A PHE 3.7 4.7 - - - -
420A PRO* 3.1 31.6 - - + -
421A CYS 2.9 39.0 - - - -
422A PHE* 4.2 2.7 - + + -
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 4.4 6.5 - - - +
91A ILE* 4.3 10.7 + - - +
281A TYR* 2.7 9.4 + - - +
283A ASN* 2.7 45.6 + - - +
284A ASP* 3.9 12.9 + - - +
288A GLU* 3.3 25.8 + - - +
354A PHE* 1.3 72.4 - - - +
356A GLN* 1.3 81.8 + - - +
357A GLY* 2.6 37.1 + - - +
359A ASP 3.8 0.7 - - - -
383A TRP* 3.2 41.7 - - + +
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Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.0 7.3 + - - +
92A CYS 3.0 25.7 + - - -
93A ASP* 3.8 6.9 - - - +
94A ALA* 3.4 23.6 + - - +
97A PHE* 6.3 0.2 - - - -
354A PHE* 3.9 12.7 - - - +
355A ARG* 1.3 90.0 + - - +
357A GLY* 1.3 55.1 + - - +
359A ASP* 2.3 53.7 + - + +
361A TRP* 3.2 37.3 + - + +
378A ARG* 3.2 29.7 + - - +
420A PRO* 5.0 2.9 - - - +
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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