Contacts of the strand formed by residues 354 - 359 (chain A) in PDB entry 3HO5
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 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A GLU* 3.7 7.4 + - - -
285A LEU* 3.4 26.6 - - - +
352A HIS 3.7 1.6 - - - -
353A LEU* 1.3 78.8 - - - +
355A GLY* 1.3 58.4 + - - -
356A GLN 3.6 2.5 - - - -
368A ILE 3.9 7.2 - - - -
370A GLY* 4.0 5.4 - - - -
432A PRO* 5.0 16.3 - - - +
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Residues in contact with GLY 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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285A LEU* 4.4 9.2 - - - -
286A SER* 3.3 3.8 - - - -
302A SER* 2.6 33.7 + - - -
319A LEU* 4.4 1.3 - - - -
353A LEU 3.7 1.8 + - - -
354A GLY* 1.3 73.5 - - - -
356A GLN* 1.3 67.5 + - - +
357A LEU* 3.2 4.9 + - - +
367A ILE* 5.0 0.9 - - - -
368A ILE 2.8 15.0 + - - -
369A LEU* 4.3 15.9 - - - +
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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
----------------------------------------------------------
285A LEU 5.5 0.2 - - - -
286A SER* 3.7 10.1 - - - +
354A GLY* 3.6 2.5 - - - -
355A GLY* 1.3 76.3 - - - +
357A LEU* 1.3 67.5 + - - +
358A LEU* 4.2 10.9 - - + +
366A TYR 3.7 1.0 - - - +
367A ILE* 3.5 3.6 - - - -
368A ILE* 2.9 51.5 + - + +
433A GLY 3.7 2.4 - - - +
434A ARG* 3.6 26.7 - - + +
435A CYS* 2.8 57.9 + - - +
437A VAL* 4.5 1.8 - - - +
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Residues in contact with LEU 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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286A SER* 2.9 19.6 + - - +
287A LEU 4.4 2.6 - - - +
288A ALA* 3.8 19.1 - - + +
300A TYR* 3.4 44.2 - - + +
301A VAL 3.8 2.7 - - - +
302A SER* 3.7 24.7 - - - +
321A VAL* 4.3 10.1 - - + -
355A GLY 3.5 17.9 - - - +
356A GLN* 1.3 79.6 + - - +
358A LEU* 1.3 66.3 + - - +
365A LEU* 4.5 4.7 - - + -
366A TYR 3.4 3.1 - - - +
367A ILE* 3.5 33.4 - - + -
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Residues in contact with LEU 358 (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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288A ALA* 4.4 5.8 - - - -
356A GLN* 4.2 8.1 - - - +
357A LEU* 1.3 77.3 - - - +
359A PHE* 1.3 64.0 + - - +
360A GLY* 4.0 8.3 - - - +
365A LEU* 3.5 6.4 - - - +
366A TYR* 2.6 68.7 + - + +
368A ILE* 3.7 28.5 - - + -
437A VAL* 3.7 39.3 - - + -
439A ARG* 4.8 8.7 - - - +
448A LEU* 4.6 7.6 - - + -
450A ILE* 5.2 4.9 - - + -
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Residues in contact with PHE 359 (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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288A ALA* 4.6 7.1 - - + +
289A PHE 3.2 28.0 - - - +
290A HIS* 3.9 1.1 - + - -
291A PRO* 3.6 29.4 - - + -
300A TYR* 3.6 37.5 - + - -
358A LEU* 1.3 74.8 - - - +
360A GLY* 1.3 58.7 + - - +
363A GLY 3.3 28.3 - - - -
364A PHE 3.5 7.6 - - - -
365A LEU* 3.5 32.3 - - + -
397A VAL* 4.0 15.5 - - + -
439A ARG* 2.3 35.0 + - - +
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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