Contacts of the strand formed by residues 343 - 352 (chain A) in PDB entry 1ORH
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 GLU 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A PHE 3.6 7.0 - - - +
338A LYS* 3.0 44.7 + - + +
342A CYS* 1.3 81.5 - - - +
344A LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASP* 4.3 23.8 - - + +
304A TYR 3.9 11.7 - - - +
305A LEU* 3.1 36.1 - - + -
335A LEU* 4.3 2.8 - - + +
336A ASP* 3.8 0.9 + - - +
337A PHE* 2.8 40.8 + - + +
342A CYS* 4.3 10.7 - - - -
343A GLU* 1.3 77.8 - - - +
345A SER* 1.3 87.3 + - - +
346A CYS* 4.0 19.1 - - + -
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A LEU 3.2 10.3 - - - -
336A ASP* 3.5 20.2 - - - -
344A LEU* 1.3 78.9 - - - +
346A CYS* 1.3 65.3 + - - +
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Residues in contact with CYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A MET* 5.6 5.6 - - - -
303A ASP* 5.3 7.6 - - - +
333A ILE 5.4 1.6 - - - -
334A ASP* 3.2 5.7 - - - +
335A LEU* 3.0 61.2 + - - +
344A LEU* 4.0 17.3 - - + -
345A SER* 1.3 76.2 - - - +
347A SER* 1.3 62.1 + - - +
348A THR* 4.8 9.6 - - - +
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 5.3 0.5 + - - -
332A THR* 4.2 10.0 - - - +
333A ILE 3.6 1.3 - - - -
334A ASP* 2.8 24.5 + - - -
346A CYS* 1.3 76.1 - - - +
348A THR* 1.3 65.6 + - - +
349A ASP* 4.9 2.6 + - - -
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 4.3 9.6 - - + -
215A LYS* 3.9 19.1 - - + +
300A TYR 4.9 0.2 - - - +
301A MET* 5.3 3.5 - - - +
302A GLU* 5.1 11.5 + - + +
332A THR* 3.5 1.9 - - - -
333A ILE* 3.0 35.9 + - - -
346A CYS* 4.8 9.4 - - - +
347A SER* 1.3 79.9 + - - +
349A ASP* 1.3 70.0 + - - +
350A TYR* 3.5 38.4 + - + +
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 2.8 43.4 + - - +
331A PHE 3.3 2.5 - - - -
332A THR* 2.6 38.3 + - - +
347A SER* 4.9 2.6 + - - -
348A THR* 1.3 74.4 - - - +
350A TYR* 1.3 63.5 + - - +
1B GLY* 3.4 21.6 + - - +
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Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.3 28.0 - - + -
215A LYS* 3.2 13.5 - - - +
217A PRO* 3.8 17.9 - - + -
299A PHE* 4.0 26.4 + + + +
300A TYR 2.6 35.4 + - - -
301A MET* 4.2 4.5 - - - +
329A LEU 4.5 0.2 - - - -
330A ASP* 3.4 3.6 - - - -
331A PHE* 2.9 46.1 + - + +
333A ILE* 4.0 22.8 - - + +
348A THR* 3.5 41.8 - - + +
349A ASP* 1.3 75.2 - - - +
351A ARG* 1.3 62.0 + - - +
352A MET 4.2 0.2 - - - -
1B GLY* 4.0 4.7 + - - -
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 3.0 13.2 + - + +
216A GLU* 4.2 6.4 - - - +
217A PRO* 3.8 10.9 - - - +
320A ARG* 5.7 1.0 - - - +
322A ASN* 2.9 30.9 + - - +
328A ASP* 4.4 4.5 - - - +
329A LEU 3.2 5.8 - - - +
330A ASP* 3.8 16.3 + - - +
350A TYR* 1.3 75.4 - - - +
352A MET* 1.3 60.7 + - - +
353A ARG* 3.0 30.1 + - - +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 4.6 4.3 - - + -
149A CYS* 4.3 11.2 - - - -
152A TYR* 3.4 57.5 - - + -
216A GLU* 5.4 0.2 - - - -
217A PRO* 3.6 33.2 - - + +
219A VAL* 4.1 25.4 - - + -
297A THR* 4.3 14.6 - - + +
328A ASP* 3.9 0.7 - - - +
329A LEU* 2.7 24.6 + - + +
331A PHE* 3.7 21.7 - - + -
350A TYR 4.2 0.4 - - - -
351A ARG* 1.3 66.5 - - - +
353A ARG* 1.3 75.9 + - - +
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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