Contacts of the strand formed by residues 404 - 410 (chain A) in PDB entry 5W6V
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 THR 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU 4.0 0.2 - - - +
39A LEU* 3.5 3.3 - - - -
40A ALA* 3.0 29.8 + - - +
42A TYR* 3.1 25.7 + - - -
43A PHE* 4.3 0.2 - - - -
44A GLU* 4.1 15.4 + - - +
212A MET* 3.2 34.0 - - + +
400A LYS* 6.1 3.0 - - - +
402A ASP 3.6 1.7 + - - -
403A MET* 1.3 73.2 - - - +
405A GLU* 1.3 74.6 + - - +
406A VAL* 5.0 1.1 - - + -
737A ASN* 4.9 9.4 - - + +
738A ILE* 4.3 13.9 - - + -
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Residues in contact with GLU 405 (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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37A LYS* 4.4 14.9 + - - -
38A LEU 3.4 8.7 - - - +
39A LEU* 3.7 21.0 - - + +
403A MET 4.0 5.1 - - - +
404A THR* 1.3 82.1 - - - +
406A VAL* 1.3 62.8 + - - +
716A ALA* 6.4 0.9 - - + -
737A ASN* 3.7 11.4 + - - -
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Residues in contact with VAL 406 (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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37A LYS* 5.0 0.2 - - - -
38A LEU* 2.8 55.2 + - + +
40A ALA* 4.6 18.4 - - + -
404A THR* 4.7 1.3 - - + +
405A GLU* 1.3 76.5 - - - +
407A THR* 1.3 66.3 + - - +
408A GLY 4.7 0.2 - - - +
713A LEU* 4.7 7.4 - - + -
734A VAL* 4.1 14.1 - - + -
736A THR* 3.9 17.5 - - - +
737A ASN* 3.5 37.0 - - + +
738A ILE* 4.8 5.4 - - + -
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Residues in contact with THR 407 (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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35A PRO* 4.0 20.4 - - + -
36A ILE 3.5 14.6 - - - +
37A LYS* 4.3 15.4 - - + +
406A VAL* 1.3 81.4 - - - +
408A GLY* 1.3 68.5 + - - +
409A ARG* 5.3 2.3 - - + +
734A VAL* 5.7 0.3 - - - +
736A THR* 4.3 8.0 + - - -
737A ASN* 5.1 0.6 + - - -
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Residues in contact with GLY 408 (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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35A PRO* 3.3 5.2 - - - +
36A ILE* 2.7 43.6 + - - -
38A LEU* 3.8 15.3 - - - +
406A VAL* 3.7 3.4 + - - +
407A THR* 1.3 74.6 - - - +
409A ARG* 1.3 63.0 + - - +
733A THR 3.2 14.4 - - - -
734A VAL* 4.2 5.2 - - - -
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Residues in contact with ARG 409 (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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29A ILE* 5.5 0.6 - - - +
30A GLY* 3.4 32.0 + - - -
31A THR* 3.7 9.4 - - - +
32A VAL 2.9 36.9 + - - +
33A GLY* 4.2 8.5 - - - +
34A LYS 3.3 6.7 - - - +
35A PRO* 5.0 4.0 - - + -
36A ILE* 4.1 0.4 - - - +
407A THR* 5.3 1.6 - - + +
408A GLY* 1.3 80.7 - - - +
410A VAL* 1.3 60.4 + - - +
411A LEU* 3.5 11.9 + - + +
731A GLY 3.1 3.3 - - - +
732A THR* 4.2 1.1 - - - -
733A THR* 2.6 49.5 + - - +
735A ASP* 3.2 33.7 + - - +
775A ASP* 3.7 2.8 + - - -
778A GLN* 2.8 30.3 + - - -
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Residues in contact with VAL 410 (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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33A GLY* 3.3 3.0 - - - -
34A LYS* 2.8 56.5 + - + +
36A ILE* 3.7 24.5 - - + -
409A ARG* 1.3 69.8 - - - +
411A LEU* 1.3 69.1 + - - +
412A PRO* 3.7 0.3 - - - +
729A PRO* 3.8 30.1 - - + -
730A ALA 3.6 24.0 - - - +
731A GLY 3.5 6.3 - - - -
732A THR* 4.1 2.2 - - - +
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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