Contacts of the helix formed by residues 83 - 91 (chain G) in PDB entry 4UIS
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 LYS 83 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ASN* 2.8 22.3 + - - +
82G ALA* 1.3 80.0 - - + +
84G LEU* 1.3 63.4 + - - +
85G LYS 3.3 0.9 - - - -
86G PRO* 3.2 18.0 - - - +
87G VAL* 3.6 12.1 - - + +
112G ALA* 3.1 42.7 - - - +
115G THR* 3.6 25.6 - - + -
118G LEU* 4.7 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 3.6 25.4 - - + +
81G ASN* 3.3 29.0 - - + +
82G ALA 3.7 0.4 - - - -
83G LYS* 1.3 76.4 - - - +
85G LYS* 1.3 53.4 + - - +
87G VAL* 3.1 5.6 + - - +
88G TYR* 2.7 36.8 + - - +
99G LEU* 4.0 11.4 - - + +
103G VAL* 3.7 27.6 - - + -
108G GLU* 3.9 14.4 - - + +
111G VAL* 3.4 31.2 - - + +
112G ALA* 4.9 0.4 - - - -
118G LEU* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ILE* 4.4 4.2 + - - +
79G LEU* 4.1 36.1 - - + +
81G ASN 3.9 14.6 + - - +
82G ALA 5.0 0.4 - - - +
83G LYS 3.3 0.2 - - - -
84G LEU* 1.3 77.9 - - - +
86G PRO* 1.4 70.5 - - + +
88G TYR* 3.2 8.8 + - + +
89G ASP* 2.9 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ALA 3.7 13.7 - - - +
83G LYS* 3.2 19.3 - - - +
85G LYS* 1.4 95.6 - - + +
87G VAL* 1.3 55.5 + - - +
89G ASP* 3.2 14.3 + - + +
90G SER* 2.9 26.3 + - - -
122G GLN* 3.3 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G LYS 3.6 15.3 - - - +
84G LEU* 3.1 8.6 + - - +
86G PRO* 1.3 72.0 - - - +
88G TYR* 1.3 60.6 + - - +
89G ASP 3.1 1.8 - - - -
90G SER* 2.7 21.2 + - - -
91G LEU* 3.0 29.6 + - + +
99G LEU* 4.6 4.3 - - + -
118G LEU* 3.5 57.2 - - + +
121G LEU* 3.9 24.0 - - + -
122G GLN* 4.2 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G VAL* 5.4 9.4 - - + +
78G ILE* 4.4 15.5 - - + -
79G LEU* 4.6 21.5 - - + -
84G LEU 2.7 20.2 + - - +
85G LYS* 3.5 8.5 - - + +
87G VAL* 1.3 74.1 - - - +
89G ASP* 1.3 68.0 + - - +
91G LEU* 4.0 2.4 - - - +
96G ARG* 2.8 72.8 + - + +
99G LEU* 3.6 22.4 - - + +
100G ILE* 4.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LYS* 2.9 37.4 + - - +
86G PRO* 3.2 15.3 - - + +
87G VAL 3.1 0.2 - - - -
88G TYR* 1.3 88.1 - - - +
90G SER* 1.3 59.5 + - - +
96G ARG* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G PRO 2.9 11.5 + - - -
87G VAL* 2.7 28.4 + - - +
89G ASP* 1.3 74.0 - - - +
91G LEU* 1.3 61.7 + - - +
92G ASP 3.7 0.2 + - - -
121G LEU 3.6 8.9 + - - -
122G GLN* 3.3 38.1 + - - -
124G LYS* 2.2 38.9 + - - +
126G TRP* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G VAL* 3.0 24.1 + - + +
88G TYR* 4.5 0.7 - - - -
89G ASP 3.3 0.6 - - - +
90G SER* 1.3 78.0 - - - +
92G ASP* 1.3 59.0 + - - +
95G ARG* 3.4 27.4 - - + +
96G ARG* 2.6 50.4 + - + -
99G LEU* 3.6 24.7 - - + -
121G LEU* 4.4 10.1 - - + -
126G TRP* 3.3 32.5 - - + -
153G PHE* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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