Contacts of the strand formed by residues 389 - 394 (chain A) in PDB entry 5KQF
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 PHE 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU 3.9 6.4 - - - +
201A GLN* 4.4 4.7 - - - -
202A LEU 4.6 0.7 + - - -
346A ILE* 3.6 28.5 - - + -
347A THR 3.5 23.1 - - - -
348A ILE* 3.6 16.8 - - + -
385A ILE* 3.0 34.5 - - + -
386A MET* 2.8 20.5 + - - +
387A GLU 3.3 1.4 + - - -
388A GLY* 1.3 86.1 - - - +
390A TYR* 1.3 67.0 + - - +
391A VAL* 3.8 13.9 + - + +
402A PHE* 4.2 14.8 - + + -
403A ALA 3.2 9.9 - - - +
404A VAL* 4.3 1.1 - - - -
405A SER* 3.5 10.2 + - - -
416A ALA* 4.2 4.3 - - + -
417A ALA 3.5 23.6 - - - -
418A VAL* 3.6 21.5 - - + -
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Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A SER* 2.6 35.6 + - - -
200A LEU 3.7 17.9 - - - -
201A GLN* 3.8 13.5 - - + +
223A ILE* 3.8 4.1 - - + +
227A ILE* 3.4 16.9 - - + -
228A ASP 2.9 26.9 + - - -
231A LEU* 3.6 28.0 - - + +
232A TYR* 3.2 51.1 - + + -
236A LEU* 4.2 3.7 - - + +
389A PHE* 1.3 72.4 - - - +
391A VAL* 1.3 58.2 + - - +
392A VAL* 4.0 13.9 + - + -
401A GLY 3.6 0.9 - - - +
402A PHE* 3.5 5.4 - - - -
403A ALA* 2.8 28.4 + - + +
405A SER* 3.7 4.9 - - - -
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Residues in contact with VAL 391 (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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199A SER* 3.2 2.7 - - - -
200A LEU 2.8 40.1 + - - +
275A VAL* 4.4 4.3 - - + -
386A MET* 4.2 25.6 - - + -
389A PHE* 3.9 15.5 - - + +
390A TYR* 1.3 77.2 - - - +
392A VAL* 1.3 64.3 + - - +
393A PHE* 3.5 31.0 - - + -
400A ILE* 3.6 23.8 - - + -
401A GLY 3.3 3.4 - - - +
402A PHE* 4.1 24.9 - - + -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.8 33.4 - - + -
198A PHE 3.9 2.7 - - - +
199A SER* 3.9 13.7 - - - -
227A ILE* 3.8 14.8 - - + -
236A LEU* 3.8 30.3 - - + -
238A TYR* 4.5 6.7 - - + -
390A TYR* 4.0 12.6 - - + -
391A VAL* 1.3 73.9 - - - +
393A PHE* 1.3 61.4 + - - +
394A ASP* 3.2 11.4 + - + +
400A ILE* 3.2 9.5 - - - +
401A GLY* 2.8 43.0 + - - +
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Residues in contact with PHE 393 (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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81A THR* 3.8 15.7 - - + -
197A LEU* 3.4 1.4 - - - -
198A PHE* 2.7 67.2 + + + +
200A LEU* 3.8 19.3 - - + -
241A ILE* 5.7 0.4 - - - -
247A TYR* 3.8 47.6 - + + -
275A VAL* 3.7 33.0 - - + -
386A MET* 3.8 7.4 - - + -
391A VAL* 3.5 28.7 - - + -
392A VAL* 1.3 69.2 - - - +
394A ASP* 1.3 59.7 + - - +
395A ARG* 3.1 12.2 + - + +
399A ARG 4.4 1.8 - - - -
400A ILE* 4.3 10.5 - - + -
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Residues in contact with ASP 394 (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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197A LEU* 3.8 28.4 - - + +
238A TYR* 4.1 5.8 + - + -
241A ILE* 5.0 0.9 - - - -
392A VAL* 3.2 8.7 + - + -
393A PHE* 1.3 69.8 - - - +
395A ARG* 1.3 60.9 + - - +
396A ALA* 3.7 10.9 + - - +
397A ARG* 3.4 21.8 + - - +
398A LYS 3.1 16.8 + - - -
399A ARG* 2.8 64.3 + - + +
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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