Contacts of the strand formed by residues 406 - 409 (chain B) in PDB entry 6DWN
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 CYS 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B THR* 5.0 7.4 - - + -
82B PRO 4.0 14.0 + - - +
83B VAL* 3.5 11.3 - - + -
84B VAL 2.9 24.1 + - - -
107B PRO* 3.7 33.7 - - + -
109B LEU* 5.1 2.5 - - + -
236B PHE* 5.0 8.5 - - - -
387B PRO* 4.4 0.9 - - - -
388B HIS 3.7 4.5 - - - -
389B SER* 4.7 1.1 - - - +
404B GLY 3.4 4.9 + - - +
405B ARG* 1.3 78.6 - - - +
407B VAL* 1.3 63.7 + - - +
408B PHE* 3.8 28.0 - - - -
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 3.1 19.3 - - + +
86B LEU* 3.6 35.9 - - + -
96B LEU* 6.5 0.2 - - + -
103B PHE* 4.2 12.8 - - + -
387B PRO* 3.6 0.3 - - - +
388B HIS* 2.8 48.6 + - + +
390B THR* 4.1 20.9 - - + +
401B ILE* 4.8 1.6 - - + -
405B ARG* 3.5 15.0 - - + +
406B CYS* 1.3 80.8 - - - +
408B PHE* 1.3 72.2 + - - +
409B VAL* 4.3 4.7 + - + -
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 5.4 2.0 - - + -
63B LEU* 4.5 18.2 - - + -
76B ILE* 5.3 2.2 - - + -
78B ILE* 4.2 12.3 - - + -
83B VAL* 3.7 22.2 - - + -
84B VAL 2.7 12.7 + - - +
85B VAL* 4.3 10.3 - - + -
86B LEU* 2.7 35.9 + - - +
109B LEU* 5.8 0.4 - - + -
230B SER* 3.9 19.5 - - - -
231B GLY* 3.9 23.1 - - - -
236B PHE* 4.3 17.0 - + - -
384B PHE* 4.3 15.5 - + + -
385B THR 5.8 0.4 - - - -
387B PRO* 3.7 31.4 - - + -
406B CYS* 3.8 13.0 - - - -
407B VAL* 1.3 81.1 - - - +
409B VAL* 1.3 57.7 + - - +
410B ASN 4.1 0.4 - - - -
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.8 16.4 - - + -
92B ILE* 3.7 38.1 - - + -
96B LEU* 4.2 13.5 - - + -
384B PHE* 3.3 8.4 - - - -
385B THR* 3.3 53.9 + - + +
387B PRO* 5.9 0.2 - - - +
388B HIS* 3.8 19.3 - - + -
407B VAL* 4.7 2.7 - - + -
408B PHE* 1.3 78.6 - - - +
410B ASN* 1.3 59.5 + - - +
411B GLN* 3.2 12.0 + - + -
414B ILE* 5.7 0.2 - - + -
448B ILE* 6.4 0.4 - - + -
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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