Contacts of the strand formed by residues 4604 - 4612 (chain B) in PDB entry 5NUG
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 VAL4604 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4603B SER* 1.3 83.3 - - - +
4605B VAL* 1.3 67.2 + - - +
4606B THR* 3.8 7.5 + - - +
4623B ASP* 5.6 7.9 - - + -
4624B PHE 3.4 15.5 - - - +
4625B GLU* 4.3 11.7 - - + -
4626B ILE* 4.6 3.8 - - - +
4632B PRO* 5.4 6.2 - - - +
4636B TYR* 4.2 10.0 + - - -
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Residues in contact with VAL4605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4575B LEU* 4.6 6.3 - - + +
4604B VAL* 1.3 73.1 - - - +
4606B THR* 1.3 63.1 + - - +
4607B LEU* 3.7 9.6 - - + -
4622B VAL 3.8 0.5 - - - +
4623B ASP* 3.4 4.5 - - - +
4624B PHE* 2.8 42.3 + - + +
4626B ILE* 3.8 40.4 - - + -
4632B PRO* 5.3 2.5 - - + -
4635B PHE* 2.4 65.5 - - + -
4636B TYR* 4.8 5.2 - - + -
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Residues in contact with THR4606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4260B PHE* 4.8 5.4 - - + -
4263B ARG* 2.7 38.6 + - - +
4604B VAL* 3.8 9.1 + - - +
4605B VAL* 1.3 77.4 + - - +
4607B LEU* 1.3 67.0 + - - +
4621B THR* 4.4 16.6 - - + -
4622B VAL 3.4 11.7 - - - +
4623B ASP* 5.0 4.8 - - + +
4636B TYR* 4.1 12.5 + - - -
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Residues in contact with LEU4607 (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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4260B PHE* 3.2 15.4 - - - -
4263B ARG* 6.2 0.2 - - - +
4565B LEU* 4.5 4.9 - - + -
4575B LEU* 3.9 11.2 - - + -
4605B VAL* 4.1 1.8 - - + -
4606B THR* 1.3 72.8 - - - +
4608B PRO* 1.3 73.1 - - + +
4621B THR* 3.5 1.6 - - - -
4622B VAL* 2.8 32.7 + - + +
4624B PHE* 3.4 35.2 - - + -
4635B PHE* 2.7 44.0 - - + -
4640B VAL* 3.5 28.5 - - + +
4641B ALA* 4.8 0.9 - - - -
4642B VAL* 4.0 15.9 - - + -
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Residues in contact with PRO4608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4260B PHE* 3.4 34.8 - - + -
4263B ARG* 5.2 2.9 - - - +
4606B THR 4.5 0.4 - - - +
4607B LEU* 1.3 91.7 - - + +
4609B VAL* 1.3 63.4 - - - +
4610B TYR* 3.6 26.7 - - + +
4615B ARG* 5.5 1.1 - - - +
4618B LEU* 3.4 22.2 - - + -
4620B PHE 3.9 2.7 - - - +
4640B VAL 3.6 15.0 - - - +
4641B ALA* 3.6 5.9 - - + +
4642B VAL* 3.1 21.7 + - - +
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Residues in contact with VAL4609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4511B LEU* 5.1 0.2 - - + -
4563B LEU* 5.5 1.1 - - + -
4608B PRO* 1.3 74.3 - - - +
4610B TYR* 1.3 64.6 + - - +
4618B LEU* 3.5 3.0 - - - +
4619B ILE* 2.8 30.9 + - + +
4620B PHE* 2.8 46.2 + - + +
4622B VAL* 2.9 38.6 - - + -
4642B VAL* 3.4 35.9 - - + +
4644B CYS* 4.1 13.5 - - - -
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Residues in contact with TYR4610 (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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4202B SER* 3.1 22.5 + - - -
4258B ASN* 4.4 9.6 + - - -
4260B PHE* 4.4 11.3 - - - +
4608B PRO* 3.6 28.9 - - + +
4609B VAL* 1.3 77.7 - - - +
4611B LEU* 1.3 64.7 + - - +
4612B ASN 4.0 7.2 - - - +
4615B ARG* 3.6 71.8 + - - -
4616B ALA 4.8 0.7 - - - -
4617B ASP 3.8 3.4 - - - +
4618B LEU* 3.6 35.2 - - + +
4619B ILE* 3.7 5.2 - - - +
4641B ALA* 3.8 11.9 - - + -
4642B VAL 2.8 18.4 + - - +
4643B LEU* 3.8 2.8 - - + -
4644B CYS* 3.7 10.4 + - - -
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Residues in contact with LEU4611 (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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4468B THR* 3.4 43.1 - - + +
4485B ARG* 5.7 2.7 - - - +
4511B LEU* 5.6 0.9 - - + +
4512B GLY* 5.5 4.9 - - - +
4514B LEU 5.8 2.0 - - - +
4515B PHE 5.5 3.1 - - - +
4517B PRO* 4.4 23.8 - - + -
4610B TYR* 1.3 76.4 - - - +
4612B ASN* 1.3 69.2 + - + +
4617B ASP* 3.1 36.9 + - + +
4619B ILE* 3.7 10.7 - - + +
4644B CYS* 3.6 6.5 + - + +
4645B THR* 3.0 46.9 + - - +
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Residues in contact with ASN4612 (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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4468B THR* 4.8 4.9 - - - +
4470B PRO* 3.5 31.4 - - + +
4610B TYR* 3.5 0.9 - - - +
4611B LEU* 1.3 96.8 - - + +
4613B PHE* 1.3 69.0 + - + +
4614B THR* 2.7 47.6 + - - +
4615B ARG* 3.1 13.0 + - - +
4616B ALA* 5.9 0.8 - - - +
4617B ASP 6.1 1.0 - - - +
4643B LEU* 2.9 22.1 - - - +
4645B THR* 3.9 26.0 - - + +
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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