Contacts of the strand formed by residues 412 - 418 (chain A) in PDB entry 4U7D
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 ALA 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN 3.0 7.0 + - - +
286A LEU* 3.5 22.8 - - + -
287A TYR* 2.7 32.4 + - - +
383A VAL 3.9 1.8 - - - +
384A ARG* 3.2 21.8 - - - +
405A ALA* 4.3 2.9 - - + -
406A GLY* 3.9 20.6 - - - +
411A LYS* 1.3 76.2 - - - +
413A ASP* 1.3 62.7 + - - +
474A MET* 5.1 0.5 - - - +
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 3.2 28.6 - - + +
311A ARG* 3.8 14.2 + - - -
312A TYR* 2.7 46.0 + - + +
384A ARG 2.8 9.8 + - - +
385A PHE* 3.2 3.1 - - + +
386A VAL 2.9 25.3 + - - +
405A ALA* 4.5 0.7 - - - +
412A ALA* 1.3 76.3 + - - +
414A CYS* 1.3 63.6 + - - +
415A ILE* 4.1 6.5 - - + -
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Residues in contact with CYS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.1 15.9 - - - -
287A TYR 2.6 16.6 + - - +
288A TYR* 3.6 28.9 - - + -
289A GLU 3.1 26.7 + - - +
386A VAL* 3.4 7.4 - - - +
398A TYR* 3.6 12.5 + - - +
402A SER* 3.8 28.5 - - - -
405A ALA* 4.1 10.5 - - - -
413A ASP* 1.3 78.5 - - - +
415A ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 5.7 1.8 - - + -
289A GLU* 3.6 15.0 - - + +
291A ARG* 3.8 39.9 - - + +
307A LEU* 4.6 9.4 - - + -
311A ARG* 4.0 15.3 - - - +
312A TYR* 3.3 31.9 - - + +
385A PHE* 6.2 0.4 - - + -
386A VAL 2.9 10.0 + - - +
387A ILE* 3.2 18.0 - - + +
388A HIS 2.7 30.6 + - - -
398A TYR* 4.5 1.1 - - - -
413A ASP* 4.5 4.0 - - + -
414A CYS* 1.3 81.2 - - - +
416A LEU* 1.3 57.1 + - - +
417A TYR* 4.3 14.4 - - + +
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Residues in contact with LEU 416 (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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289A GLU 3.0 12.2 + - - +
290A VAL* 3.4 8.8 - - + +
291A ARG 2.9 28.1 + - - +
388A HIS* 3.8 16.4 - - + -
391A MET* 4.0 15.9 - - + +
398A TYR* 3.7 35.9 - - + +
414A CYS 4.1 0.4 + - - -
415A ILE* 1.3 73.8 - - - +
417A TYR* 1.3 79.8 + - - +
418A TYR* 3.6 10.1 + - + +
443A MET* 4.4 13.2 - - - -
446A TYR* 4.4 12.1 - - + -
447A CYS* 4.0 25.6 - - - -
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Residues in contact with TYR 417 (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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291A ARG* 3.4 36.7 + - + -
292A GLN 3.5 21.5 - - - -
293A LYS* 3.9 8.9 - - + +
294A PRO* 4.9 1.6 - - + -
300A PHE* 3.3 47.1 - + + -
303A ASP* 4.5 16.1 + - + +
304A ILE* 4.5 7.1 - - + +
307A LEU* 3.5 26.3 - - + +
387A ILE* 3.9 29.6 - - + -
388A HIS 2.8 15.0 + - - +
389A HIS 3.7 12.0 - - - +
390A SER* 4.1 6.6 - - - -
391A MET 4.1 1.0 + - - -
415A ILE* 4.3 8.3 - - + -
416A LEU* 1.3 77.8 - - - +
418A TYR* 1.3 62.6 + - - +
419A GLY 3.6 2.8 + - - -
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Residues in contact with TYR 418 (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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290A VAL* 3.9 15.5 - - + -
291A ARG 2.9 12.6 + - - +
292A GLN* 3.2 21.3 + - - -
293A LYS* 2.8 24.2 + - - -
391A MET* 3.8 27.1 - - + -
416A LEU* 3.6 7.5 + - + -
417A TYR* 1.3 70.4 - - - +
419A GLY* 1.3 64.3 + - - +
420A PHE* 4.9 6.8 - - - -
423A ILE* 4.1 11.7 - - + +
444A VAL* 4.1 3.8 - - + +
447A CYS* 3.7 40.8 - - + -
448A GLN* 2.8 31.7 + - + +
543A GLU 5.1 0.3 + - - -
544A LYS* 5.1 8.4 - - + -
547A ALA* 3.6 15.9 - - - +
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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
------------------------------------------------------------
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