Contacts of the helix formed by residues 3689 - 3696 (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 PRO3689 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2997B SER* 6.5 0.4 - - - -
3641B TYR* 6.4 1.1 - - + -
3687B GLU* 3.7 5.3 - - + +
3688B PHE* 1.3 88.4 - - + +
3690B PRO* 1.3 70.5 - - + +
3691B ASP* 4.4 6.5 - - + +
3692B LEU* 2.9 45.2 + - + +
3693B CYS 2.9 10.2 + - - -
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Residues in contact with PRO3690 (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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2938B VAL* 5.8 0.4 - - + -
2939B SER* 2.8 17.4 + - - +
3069B ASN* 4.0 30.1 - - + +
3170B ALA* 4.3 20.4 - - + +
3172B THR* 4.9 1.2 - - - +
3688B PHE 3.7 2.3 - - - +
3689B PRO* 1.3 86.5 - - + +
3691B ASP* 1.3 59.6 + - + +
3693B CYS* 3.6 11.2 - - + +
3694B SER* 3.2 17.5 + - - -
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Residues in contact with ASP3691 (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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2939B SER* 3.5 21.6 + - - -
2995B ASP* 4.4 3.7 - - - +
2997B SER* 3.0 37.3 + - - -
3069B ASN* 5.5 2.0 + - - +
3646B ASN* 4.7 1.6 - - - +
3689B PRO* 3.0 6.9 + - + +
3690B PRO* 1.3 84.9 - - + +
3692B LEU* 1.3 62.2 + - - +
3694B SER* 3.6 5.7 + - - -
3695B ARG* 2.7 65.2 + - - +
4805B ADP 4.3 2.3 + - - -
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Residues in contact with LEU3692 (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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3588B LEU* 4.5 6.1 - - + -
3638B VAL* 4.2 14.8 - - + -
3641B TYR* 3.8 48.7 - - + +
3646B ASN* 5.5 1.3 - - - +
3649B LEU* 4.2 2.7 - - + -
3679B LEU* 4.6 2.9 - - + -
3688B PHE* 3.6 32.3 - - + -
3689B PRO* 2.9 27.6 + - + +
3691B ASP* 1.3 74.5 + - - +
3693B CYS* 1.3 67.2 + - - +
3695B ARG* 3.2 16.7 + - + +
3696B VAL* 3.4 28.2 + - + +
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Residues in contact with CYS3693 (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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3169B MET* 3.7 10.1 - - + -
3170B ALA 3.5 38.1 - - - +
3175B HIS* 4.0 8.0 - - - -
3688B PHE* 4.9 4.9 - - + +
3689B PRO 2.9 13.7 + - - +
3690B PRO* 3.6 15.5 - - + +
3691B ASP 3.3 0.2 - - - -
3692B LEU* 1.3 78.3 - - - +
3694B SER* 1.3 62.4 + - - +
3695B ARG 3.3 0.2 + - - -
3696B VAL* 3.2 19.8 - - - +
3698B PHE* 3.4 35.4 - - + -
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Residues in contact with SER3694 (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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2939B SER* 2.9 29.0 + - - -
2940B GLY* 4.1 6.1 - - - -
3172B THR* 2.6 42.2 - - - +
3174B ARG* 3.2 21.8 - - - +
3175B HIS* 4.4 3.3 - - - -
3585B ARG* 3.4 14.2 + - - -
3690B PRO 3.2 5.7 + - - -
3691B ASP 3.9 4.7 - - - -
3692B LEU 3.3 0.4 - - - -
3693B CYS* 1.3 78.4 - - - +
3695B ARG* 1.3 65.0 + - - +
3696B VAL 3.3 1.2 + - - -
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Residues in contact with ARG3695 (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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2944B THR* 5.8 0.8 - - - +
2995B ASP* 3.9 15.2 + - - -
2997B SER* 5.0 0.6 + - - -
2998B ASN* 5.7 1.0 - - - +
3174B ARG* 4.1 16.0 + - - +
3585B ARG* 3.7 13.1 - - - +
3586B TYR 4.1 3.5 + - - -
3646B ASN* 3.2 42.5 + - - +
3649B LEU* 4.0 27.8 - - + +
3650B ASN* 3.0 41.3 + - - +
3691B ASP* 2.7 55.7 + - - +
3692B LEU* 3.2 10.4 + - - +
3694B SER* 1.3 78.5 - - - +
3696B VAL* 1.3 62.3 + - + +
4805B ADP 4.3 11.7 + - - -
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Residues in contact with VAL3696 (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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3585B ARG* 2.7 21.6 + - - -
3586B TYR 3.3 12.6 - - - +
3588B LEU* 3.6 33.0 - - + -
3649B LEU* 3.9 18.2 - - + -
3679B LEU* 4.0 12.1 - - + -
3692B LEU* 3.4 34.8 - - + +
3693B CYS 3.2 10.0 - - - +
3694B SER 3.2 1.2 - - - -
3695B ARG* 1.3 84.2 - - - +
3697B THR* 1.3 57.8 + - - +
3698B PHE* 3.2 14.6 + - + -
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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