Contacts of the strand formed by residues 350 - 357 (chain A) in PDB entry 5H15
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 VAL 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A PHE* 3.9 7.0 - - + -
301A THR* 3.7 17.3 - - - +
303A ASP* 4.2 16.4 - - + +
304A ILE* 3.5 35.7 - - + -
331A TRP* 3.6 24.9 - - + -
332A LYS 3.7 2.2 - - - +
334A GLY 3.6 2.9 - - - -
348A SER 4.2 1.8 + - - +
349A ASN* 1.3 79.7 - - - +
351A THR* 1.3 62.2 + - - +
352A ILE* 4.3 8.3 + - + +
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Residues in contact with THR 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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331A TRP* 3.2 4.1 - - - -
332A LYS* 2.8 52.0 + - + +
334A GLY 2.7 21.2 + - - -
335A LYS* 3.2 2.9 - - - -
336A MET* 3.1 50.9 + - + -
350A VAL* 1.3 72.1 + - - +
352A ILE* 1.3 73.2 + - - +
353A LEU* 3.8 2.0 + - + +
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Residues in contact with ILE 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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303A ASP 5.0 11.2 - - - +
304A ILE* 4.8 13.7 - - + +
329A VAL* 4.1 14.4 - - + -
330A CYS 3.7 5.8 - - - +
331A TRP* 4.0 11.7 - - + -
336A MET* 4.8 3.1 - - - +
350A VAL* 4.3 5.8 + - + +
351A THR* 1.3 80.7 - - - +
353A LEU* 1.3 62.6 + - - +
354A GLY* 3.7 21.5 - - - +
355A ARG* 3.7 37.5 - - - +
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Residues in contact with LEU 353 (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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318A LEU* 3.7 35.7 - - + -
330A CYS* 2.8 17.2 + - - +
331A TRP* 3.9 21.3 - - - +
332A LYS* 4.0 7.0 - - + -
336A MET* 3.9 20.6 - - + -
351A THR* 3.9 7.0 - - + +
352A ILE* 1.3 74.6 - - - +
354A GLY* 1.3 57.1 + - - +
396A PRO* 5.8 1.2 - - - +
41C MET* 3.6 39.3 - - + -
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Residues in contact with GLY 354 (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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329A VAL* 3.9 0.2 - - - -
330A CYS* 3.0 33.8 + - - +
352A ILE* 3.6 9.3 - - - +
353A LEU* 1.3 77.6 - - - +
355A ARG* 1.3 71.9 + - - +
356A PHE* 5.6 0.2 - - - -
396A PRO* 4.5 13.7 - - - -
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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
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327A ALA* 4.5 6.3 - - + -
328A ILE 3.3 8.3 - - - +
329A VAL* 3.8 24.2 - - + +
330A CYS 4.7 0.2 - - - +
352A ILE* 3.7 38.1 - - - +
354A GLY* 1.3 80.0 - - - +
356A PHE* 1.3 60.8 + - - +
357A ASP* 3.7 26.5 + - - +
396A PRO* 3.1 21.9 - - - +
397A HIS 5.1 0.3 + - - -
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Residues in contact with PHE 356 (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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315A LEU* 5.7 2.9 - - + -
320A LEU* 4.0 21.8 - - + -
327A ALA* 4.3 0.7 - - - -
328A ILE* 2.8 51.8 + - + +
330A CYS* 4.4 11.4 - - + -
355A ARG* 1.3 70.2 - - - +
357A ASP* 1.4 60.5 + - - +
358A TYR* 3.3 10.5 - - - -
377A LEU* 4.0 13.0 - - + -
389A TRP* 3.5 48.0 - + + +
390A ASP 5.4 0.7 - - - -
391A LEU* 3.7 28.0 - - + -
393A VAL 5.5 1.1 - - - -
396A PRO* 3.6 33.2 - - + -
399A ALA* 4.4 6.5 - - + -
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Residues in contact with ASP 357 (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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326A ASN 3.5 7.4 - - - +
327A ALA* 3.7 16.8 - - - +
355A ARG* 3.7 20.6 + - - +
356A PHE* 1.4 71.8 - - - +
358A TYR* 1.3 63.9 + - - +
389A TRP* 3.6 14.1 + - - +
397A HIS* 4.8 16.8 - - + -
400A LYS* 4.1 9.5 - - - +
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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