Contacts of the helix formed by residues 4102 - 4116 (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 ALA4102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1966B ARG* 5.4 4.0 - - - +
4071B ILE* 4.1 9.2 - - + -
4072B GLY 5.5 0.4 - - - +
4077B PHE* 3.4 35.0 - - + -
4099B VAL 3.3 8.7 + - - +
4101B LEU* 1.3 82.6 - - - +
4103B PRO* 1.3 72.0 - - - +
4104B GLY 3.2 2.7 - - - -
4105B TRP* 2.9 15.2 + - + +
4106B LEU* 3.4 8.5 + - - +
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Residues in contact with PRO4103 (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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4099B VAL 4.6 0.4 - - - -
4100B HIS 4.0 7.2 - - - +
4101B LEU 3.7 3.8 - - - -
4102B ALA* 1.3 88.2 - - - +
4104B GLY* 1.3 66.0 + - - +
4106B LEU* 2.9 22.6 + - + +
4107B MET* 3.6 4.7 + - - +
4133B LYS* 3.6 48.2 - - + +
4134B VAL 4.9 0.4 - - - +
4135B PRO* 3.6 19.6 - - + +
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Residues in contact with GLY4104 (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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4102B ALA 3.0 1.8 + - - -
4103B PRO* 1.3 79.3 - - - +
4105B TRP* 1.3 61.5 + - - +
4107B MET* 3.8 9.6 + - - +
4108B GLN* 3.6 24.1 + - - +
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Residues in contact with TRP4105 (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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4071B ILE* 3.4 31.6 - - + -
4077B PHE* 3.2 47.4 - + + +
4080B ALA* 3.7 20.2 - - + -
4081B ASP* 4.1 24.1 + - - -
4084B ILE* 4.7 1.8 - - + -
4096B LEU* 3.4 12.8 - - + -
4102B ALA* 2.9 9.3 + - + +
4104B GLY* 1.3 76.2 - - - +
4106B LEU* 1.3 70.6 + - + +
4108B GLN* 3.2 22.9 + - + +
4109B LEU* 2.9 62.6 + - + +
4112B LYS* 6.4 0.4 - - - -
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Residues in contact with LEU4106 (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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4099B VAL* 3.3 53.6 - - + +
4100B HIS* 4.3 4.3 - - - +
4102B ALA 3.4 4.2 + - - +
4103B PRO* 2.9 11.2 + - + +
4105B TRP* 1.3 94.3 - - + +
4107B MET* 1.3 57.8 + - - +
4109B LEU* 3.2 9.4 + - + +
4110B GLU* 2.9 28.3 + - - +
4126B LEU* 4.2 8.7 - - + -
4128B MET* 4.1 7.4 - - + -
4134B VAL* 4.5 1.8 - - + -
4135B PRO* 4.1 20.2 - - + -
4138B LEU* 3.5 34.6 - - + +
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Residues in contact with MET4107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3639B GLU* 3.2 33.9 - - - +
3640B SER* 6.2 0.9 - - - -
4103B PRO 3.6 4.7 + - - +
4104B GLY* 4.0 9.4 - - - +
4106B LEU* 1.3 78.3 - - - +
4108B GLN* 1.3 59.7 + - + +
4110B GLU* 3.2 13.3 + - - +
4111B LYS* 2.9 42.2 + - - +
4135B PRO* 3.4 34.4 - - + +
4137B ASN* 4.1 18.4 - - + +
4138B LEU* 5.7 1.1 - - - -
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Residues in contact with GLN4108 (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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2965B ARG* 5.6 4.7 + - - -
3615B LEU* 4.9 16.8 - - + -
4104B GLY* 3.6 19.2 - - - +
4105B TRP* 3.2 27.5 + - + +
4107B MET* 1.3 76.6 - - + +
4109B LEU* 1.3 57.1 + - - +
4111B LYS* 3.2 12.0 + - + +
4112B LYS* 2.9 29.0 + - - +
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Residues in contact with LEU4109 (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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4084B ILE* 3.9 15.7 - - + -
4096B LEU* 3.6 14.6 - - + -
4105B TRP* 2.9 55.3 + - + +
4106B LEU* 3.4 13.7 - - + +
4108B GLN* 1.3 75.3 - - - +
4110B GLU* 1.3 64.4 + - - +
4112B LYS* 3.2 15.0 + - - +
4113B LEU* 2.9 33.0 + - + +
4124B LEU* 4.2 15.5 - - + -
4126B LEU* 3.9 26.9 - - + -
4138B LEU* 4.3 5.8 - - + -
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Residues in contact with GLU4110 (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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3682B ARG* 3.8 30.5 + - - +
4106B LEU 2.9 12.4 + - - +
4107B MET* 3.2 14.2 + - - +
4109B LEU* 1.3 81.2 - - - +
4111B LYS* 1.3 79.2 + - - +
4113B LEU* 3.2 11.5 + - + +
4114B HIS* 2.9 28.6 + - - +
4137B ASN* 3.5 46.6 + - - +
4138B LEU* 3.9 19.5 - - + +
4141B ALA* 4.1 11.9 - - + -
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Residues in contact with LYS4111 (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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3615B LEU* 3.5 35.0 - - + +
3637B ASP* 3.8 38.3 + - - +
3639B GLU* 3.4 28.9 + - - +
3640B SER* 4.0 15.8 - - - -
3682B ARG* 6.1 4.5 - - + -
4107B MET* 2.9 27.7 + - - +
4108B GLN* 3.4 11.1 - - - +
4110B GLU* 1.3 91.2 + - - +
4112B LYS* 1.3 56.5 + - - +
4114B HIS* 3.2 8.1 + - - +
4115B SER* 2.9 29.2 + - - -
4137B ASN* 5.0 0.7 - - - +
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Residues in contact with LYS4112 (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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4081B ASP* 2.7 46.8 + - - +
4084B ILE* 4.6 23.5 - - - +
4085B ASN* 5.5 5.1 + - - +
4105B TRP* 6.4 0.4 - - - -
4108B GLN 2.9 13.3 + - - +
4109B LEU* 3.2 15.7 + - - +
4111B LYS* 1.3 75.9 - - - +
4113B LEU* 1.3 56.8 + - - +
4115B SER* 2.6 27.6 + - - +
4116B LEU* 2.9 30.0 + - + +
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Residues in contact with LEU4113 (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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4037B PRO 5.0 0.2 - - - +
4038B ASN* 3.6 35.6 - - + +
4039B THR 4.9 0.2 - - - +
4040B PRO* 3.4 45.1 - - + -
4084B ILE* 5.6 3.8 - - + -
4109B LEU* 2.9 17.8 + - + +
4110B GLU* 3.2 13.0 - - - +
4112B LYS* 1.3 75.7 - - - +
4114B HIS* 1.3 64.2 + - - +
4116B LEU* 3.0 30.7 + - + +
4122B PHE* 4.8 11.7 - - + -
4124B LEU* 3.7 30.7 - - + -
4138B LEU* 5.5 0.2 - - + -
4141B ALA* 5.6 3.8 - - + -
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Residues in contact with HIS4114 (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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3593B SER 5.5 3.1 - - - -
3594B GLY* 5.9 4.5 - - - -
3636B GLN* 6.1 2.7 + - - -
3637B ASP* 6.1 0.9 - - - -
3682B ARG* 3.2 61.0 + - + +
3830B GLN* 5.5 2.0 - - - -
4038B ASN* 4.9 10.6 + - - +
4110B GLU* 2.9 13.5 + - - +
4111B LYS* 3.4 11.9 - - - +
4113B LEU* 1.3 79.3 - - - +
4115B SER* 1.3 63.2 + - - +
4116B LEU 3.5 2.8 + - - +
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Residues in contact with SER4115 (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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4111B LYS 2.9 13.1 + - - -
4112B LYS* 2.6 26.7 + - - +
4114B HIS* 1.3 81.3 - - - +
4116B LEU* 1.3 60.7 + - - +
4117B GLN* 3.8 2.8 + - - +
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Residues in contact with LEU4116 (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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4038B ASN* 3.8 9.9 + - - +
4084B ILE* 5.3 6.7 - - + -
4085B ASN* 5.1 11.2 - - - +
4088B VAL* 3.6 44.4 - - + -
4112B LYS* 2.9 30.3 + - + +
4113B LEU* 3.0 22.5 + - + +
4114B HIS 4.1 1.3 - - - +
4115B SER* 1.3 78.6 + - - +
4117B GLN* 1.3 68.7 + - - +
4118B PRO* 3.6 9.5 - - + +
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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