Contacts of the strand formed by residues 353 - 358 (chain A) in PDB entry 6BHG
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 LEU 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A GLY 4.0 5.8 - - - +
352A GLN* 1.3 76.6 + - - +
354A ILE* 1.3 69.5 + - - +
365A SER 3.4 15.0 - - - +
366A ARG* 3.8 28.5 - - + -
380A LEU* 4.2 13.0 - - + -
521A UNX 4.2 6.3 - - - -
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Residues in contact with ILE 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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348A LEU* 4.2 15.5 - - + -
352A GLN* 4.1 19.9 + - + +
353A LEU* 1.3 80.9 - - - +
355A LYS* 1.3 64.7 + - - +
356A THR* 3.7 13.7 - - - +
364A LYS* 4.1 0.6 - - - -
365A SER* 2.7 48.3 + - - +
367A VAL* 4.6 5.8 - - + -
377A ILE* 4.1 11.9 - - + -
395A LEU* 3.9 21.1 - - + -
397A PRO* 4.1 29.8 - - + -
518A UNX 3.6 11.2 - - - -
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Residues in contact with LYS 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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354A ILE* 1.3 76.3 - - - +
356A THR* 1.3 62.5 + - - +
362A TRP* 4.2 30.9 + - + +
363A TRP 3.2 12.1 - - - +
364A LYS* 4.4 25.8 - - + +
394A ARG 4.0 0.2 - - - +
396A GLU* 2.9 38.5 + - + +
518A UNX 2.9 18.4 - - - -
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Residues in contact with THR 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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354A ILE* 3.7 11.4 - - - +
355A LYS* 1.3 75.3 + - - +
357A GLU* 1.3 68.2 + - - +
362A TRP* 3.9 1.6 - - - -
363A TRP* 2.9 35.4 + - - +
365A SER* 2.8 21.9 + - - -
377A ILE* 3.6 9.1 - - + +
379A PHE* 3.6 29.9 - - + -
388A ILE* 3.6 24.0 - - + -
394A ARG 3.3 11.4 - - - +
395A LEU* 4.0 5.5 - - + +
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Residues in contact with GLU 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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356A THR* 1.3 77.0 - - - +
358A TRP* 1.4 75.6 + - - +
359A GLU 3.8 1.1 + - - -
360A GLY* 2.9 26.2 + - - +
361A THR 3.3 12.8 - - - +
362A TRP* 3.5 39.9 - - + +
394A ARG* 2.8 59.0 + - - +
12B GLY 4.7 2.3 - - - +
15B ALA 4.4 0.2 - - - +
16B PRO* 3.5 24.8 - - + +
17B ARG* 2.9 20.6 + - - +
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Residues in contact with TRP 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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357A GLU* 1.4 80.2 - - - +
359A GLU* 1.3 118.6 + - + +
360A GLY 3.2 0.7 - - - -
361A THR* 2.9 13.3 + - - -
363A TRP* 2.9 38.5 + + + +
379A PHE* 3.8 10.3 - + + -
382A ASP* 5.3 1.8 - - - -
386A GLU* 3.9 5.2 - - - -
394A ARG* 3.6 17.0 - - - +
524A UNX 3.8 12.8 - - - -
528A UNX 3.3 25.5 - - - -
10B SER* 2.8 36.9 + - - -
11B THR 4.1 2.4 + - - -
12B GLY* 3.8 11.6 - - - +
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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
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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