Contacts of the helix formed by residues 80 - 98 (chain G) in PDB entry 5CAY
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 ASN 80 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ASP 3.1 21.1 + - - +
77G ALA 3.8 2.5 - - - +
78G TRP 3.0 1.0 + - - -
79G ASN* 1.3 74.3 + - - +
81G THR* 1.3 58.9 + - - +
82G VAL* 2.7 37.6 + - - +
83G THR* 3.1 21.0 + - - +
84G GLU* 2.9 41.6 + - - +
494G LEU 4.0 8.1 + - - -
495G GLY 3.7 8.7 + - - -
497G TYR 2.8 29.4 + - - -
498G LYS* 4.9 2.7 - - - -
499G LEU 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LEU* 3.5 8.0 - - - +
80G ASN* 1.3 71.5 + - - +
82G VAL* 1.3 64.5 + - - +
84G GLU* 4.0 16.2 - - - +
85G GLN* 3.2 23.7 + - - +
499G LEU* 3.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G LEU* 3.8 27.5 - - + +
80G ASN* 2.7 19.8 + - - +
81G THR* 1.3 72.7 + - - +
83G THR* 1.3 56.6 + - - +
85G GLN* 3.4 3.6 + - - +
86G ALA* 3.0 25.5 + - - +
232G TYR* 4.4 11.6 - - + -
240G LEU* 4.3 9.4 - - + -
264G THR* 4.7 8.7 - - + -
494G LEU* 3.9 30.1 - - + +
497G TYR* 4.3 15.9 - - + -
498G LYS 4.4 0.2 - - - -
499G LEU* 4.0 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ALA 2.8 28.4 + - - +
78G TRP 3.7 5.2 + - - -
80G ASN* 3.1 15.4 + - - +
82G VAL* 1.3 73.2 - - - +
84G GLU* 1.3 66.5 + - - +
86G ALA* 3.2 7.9 + - - +
87G VAL* 3.0 30.2 + - - +
490G TYR 4.0 4.3 - - - +
491G ARG* 3.9 24.7 + - - -
494G LEU* 3.7 33.9 - - + +
495G GLY* 3.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 3.4 37.1 - - + +
78G TRP 3.3 13.0 - - - +
79G ASN* 3.6 1.2 - - - +
80G ASN 2.9 40.4 + - - +
81G THR* 4.1 13.6 - - - +
83G THR* 1.3 79.4 + - - +
85G GLN* 1.3 58.6 + - - +
87G VAL* 3.8 6.7 + - - +
88G GLU* 3.5 25.5 + - - +
491G ARG* 5.5 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G PRO* 3.7 12.0 - - - +
42G LEU* 2.9 60.5 + - + +
44G CYS* 5.3 0.4 - - - +
81G THR 3.2 20.2 + - - +
82G VAL 3.8 1.6 - - - +
84G GLU* 1.3 75.1 - - - +
86G ALA* 1.3 60.8 + - - +
88G GLU* 3.3 7.2 + - + +
89G ASP* 2.9 49.9 + - - +
232G TYR* 3.6 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G VAL 3.0 14.9 + - - +
83G THR* 3.2 13.7 + - - +
85G GLN* 1.3 75.2 - - - +
87G VAL* 1.3 53.1 + - - +
89G ASP* 3.3 1.0 + - - +
90G VAL* 2.8 41.5 + - - +
232G TYR* 3.3 17.2 + - + -
267G MET* 3.8 26.7 - - - -
490G TYR* 4.2 9.6 - - + +
494G LEU* 4.1 4.9 - - + -
----------------------------------------------------------
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 THR 3.0 20.1 + - - +
84G GLU* 4.0 6.1 - - - +
85G GLN 3.3 0.2 - - - -
86G ALA* 1.3 75.2 - - - +
88G GLU* 1.3 65.2 + - - +
90G VAL* 3.9 0.4 - - - -
91G TRP* 3.0 22.7 + - - +
441G TRP* 3.8 7.6 - - + -
442G HIS* 3.3 32.8 - - + +
487G ALA* 3.5 45.3 - - + +
490G TYR* 4.2 11.9 - - + -
491G ARG* 4.1 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G GLU 3.5 16.2 + - - +
85G GLN* 3.3 10.1 + - + +
87G VAL* 1.3 79.3 - - - +
89G ASP* 1.3 60.7 + - - +
91G TRP* 3.3 10.9 + - - +
92G SER* 2.9 27.4 + - - -
442G HIS* 2.9 35.4 + - - -
443G LYS* 4.8 7.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
44G CYS* 4.3 14.0 - - - +
85G GLN* 2.9 27.5 + - - +
86G ALA 3.8 1.3 - - - +
88G GLU* 1.3 78.4 - - - +
90G VAL* 1.3 59.1 + - + +
92G SER* 3.2 8.1 + - - -
93G LEU* 2.9 41.0 + - + +
232G TYR* 2.5 41.8 + - - +
267G MET* 5.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ALA 2.8 25.2 + - - +
87G VAL 3.9 2.9 - - - +
89G ASP* 1.3 69.8 - - - +
91G TRP* 1.3 57.0 + - - +
93G LEU* 3.1 8.5 + - + +
94G PHE* 2.7 33.1 + - - +
267G MET* 4.4 9.9 - - + -
269G THR* 3.2 41.7 - - + +
271G THR* 3.9 10.3 - - + -
441G TRP* 4.0 1.8 - - + -
490G TYR* 3.3 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G VAL 3.0 14.3 + - - +
88G GLU* 3.5 13.2 - - - +
90G VAL* 1.3 77.1 - - - +
92G SER* 1.3 65.4 + - - +
94G PHE* 3.3 30.0 + + - +
95G GLU* 3.4 34.2 + - + +
103G LYS* 4.0 10.5 - - - -
440G THR* 3.6 34.1 - - + -
441G TRP* 3.5 30.2 - + + -
442G HIS* 3.3 46.2 - + + -
443G LYS* 4.1 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU 2.9 13.9 + - - -
89G ASP* 3.2 13.4 + - - -
91G TRP* 1.3 82.3 - - - +
93G LEU* 1.3 64.6 + - - +
95G GLU* 3.5 12.1 + - - +
96G THR* 3.5 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G ASP* 2.9 29.1 + - + +
90G VAL* 3.5 9.0 - - + +
92G SER* 1.3 78.5 - - - +
94G PHE* 1.3 60.3 + - - +
96G THR* 3.3 8.8 + - - +
97G SER* 2.8 36.7 + - - -
225G TRP* 5.5 8.2 - - + -
227G THR 5.3 0.9 - - - +
230G PHE* 3.3 45.5 - - + -
269G THR* 3.7 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G VAL 2.7 16.5 + - - +
91G TRP* 3.3 28.7 + + - +
93G LEU* 1.3 75.6 - - - +
95G GLU* 1.3 65.0 + - + +
96G THR 3.6 0.2 + - - -
97G SER* 4.0 6.7 + - - -
98G ILE* 3.4 22.5 + - + +
271G THR* 3.4 30.3 - - + -
393G TRP* 3.5 26.0 - + - -
395G ASN* 6.1 0.2 - - - -
400G PHE* 3.7 29.8 - + - -
438G ILE* 4.3 7.6 - - + -
440G THR* 5.3 1.3 - - + -
441G TRP* 3.6 23.6 - + + +
447G ASN* 4.4 7.0 - - - -
449G TYR* 3.7 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G TRP* 3.4 39.5 + - + +
92G SER* 3.5 7.4 + - - +
93G LEU 3.3 0.6 - - - -
94G PHE* 1.3 86.4 - - + +
96G THR* 1.3 63.0 + - + +
98G ILE 3.7 3.7 - - - +
99G LYS* 4.0 2.1 - - - +
100G PRO* 3.3 32.3 - - + +
103G LYS* 3.4 24.0 - - - +
218G GLU* 4.9 5.8 - - - +
447G ASN* 3.1 25.9 + - - +
449G TYR* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G SER* 3.5 16.4 + - - +
93G LEU* 3.3 12.9 + - - +
95G GLU* 1.3 82.1 - - + +
97G SER* 1.3 67.6 + - - +
98G ILE 4.5 0.9 - - - -
99G LYS* 4.4 2.2 + - - +
223G HIS* 3.2 18.4 + - - -
225G TRP* 3.5 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LEU* 2.8 23.1 + - - -
94G PHE* 4.0 7.6 + - - -
95G GLU 3.8 0.2 - - - -
96G THR* 1.3 77.9 + - - +
98G ILE* 1.3 78.6 + - - +
223G HIS* 3.4 26.2 + - - +
224G TYR* 3.7 0.5 - - - -
225G TRP* 3.6 42.4 + - - -
228G MET* 4.2 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G PHE* 3.4 18.7 + - + +
95G GLU* 3.7 2.6 - - - +
97G SER* 1.3 82.6 + - - +
99G LYS* 1.3 63.0 + - - +
100G PRO* 3.6 7.8 - - - +
223G HIS 4.6 4.7 - - - +
224G TYR* 3.7 19.5 - - + -
395G ASN* 3.5 31.0 - - + +
398G GLY* 3.5 30.1 - - - +
400G PHE* 3.7 28.5 - - + -
449G TYR* 3.6 27.0 + - + -
453G ARG* 6.1 0.2 - - - +
----------------------------------------------------------
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