Contacts of the helix formed by residues 92 - 105 (chain G) in PDB entry 5IC4
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 THR 92 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G HIS* 4.2 12.1 - - + +
90G ASP 5.2 1.1 - - - +
91G LEU* 1.3 75.6 - - - +
93G ARG* 1.3 65.3 + - - +
94G GLU* 3.2 14.9 + - - +
95G GLU* 2.7 44.0 + - - +
96G ILE* 3.0 22.5 + - - +
129G GLY* 4.1 1.3 - - - -
130G THR* 3.3 15.9 - - - +
131G ASN* 3.2 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G THR* 1.3 72.0 - - - +
94G GLU* 1.3 81.9 + - + +
96G ILE* 3.6 2.7 + - - +
97G VAL* 3.2 28.8 + - - +
129G GLY* 3.9 4.2 - - - -
131G ASN* 2.6 35.6 + - - +
132G GLY* 3.9 15.0 - - - +
133G PRO* 3.5 35.2 + - - +
134G VAL* 3.6 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G THR* 3.2 9.2 + - - +
93G ARG* 1.3 91.9 - - + +
95G GLU* 1.3 60.7 + - + +
97G VAL* 3.5 6.2 + - - +
98G GLU* 3.0 33.6 + - - +
131G ASN* 2.9 25.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
90G ASP 3.9 4.3 - - - +
91G LEU* 3.3 26.8 - - + +
92G THR* 2.7 49.9 + - - +
94G GLU* 1.3 76.6 - - + +
96G ILE* 1.3 58.8 + - - +
98G GLU* 3.5 20.6 - - - +
99G LEU* 2.9 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ILE* 3.8 26.7 - - + -
52G ASN* 4.0 11.7 - - - +
91G LEU* 3.6 22.7 - - + -
92G THR 3.0 14.8 + - - +
93G ARG 3.9 3.8 - - - +
94G GLU 3.3 0.2 - - - -
95G GLU* 1.3 76.8 - - - +
97G VAL* 1.3 57.6 + - - +
99G LEU* 3.2 3.1 + - - +
100G MET* 2.9 31.8 + - + +
118G LEU* 5.3 4.3 - - + -
127G ILE* 5.0 9.4 - - + -
128G PHE 4.4 2.2 - - - +
129G GLY* 3.7 31.6 - - - +
134G VAL* 4.5 11.9 - - + -
139G ILE* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ARG 3.2 18.9 + - - +
94G GLU* 3.7 6.5 - - - +
96G ILE* 1.3 76.4 - - - +
98G GLU* 1.3 59.0 + - - +
100G MET 3.5 0.2 + - - -
101G ARG* 3.0 54.8 + - - +
134G VAL* 4.2 22.2 - - + -
138G LYS* 3.9 29.2 - - + +
139G ILE* 4.4 9.6 - - + -
142G PHE* 3.8 12.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G GLU* 3.0 15.2 + - - +
95G GLU* 3.5 27.7 - - - +
97G VAL* 1.3 78.5 - - - +
99G LEU* 1.3 66.2 + - - +
101G ARG* 3.9 12.0 - - - +
102G ASP* 3.1 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 4.0 18.2 - - + -
50G ILE* 4.0 11.7 - - + -
86G ARG* 5.8 1.3 - - - +
88G LYS* 3.8 36.8 - - + +
91G LEU* 3.7 24.7 - - + -
95G GLU 2.9 19.3 + - - +
96G ILE 3.4 2.7 - - - +
98G GLU* 1.3 77.2 - - + +
100G MET* 1.3 61.6 + - - +
102G ASP* 3.2 6.7 + - + +
103G VAL* 2.8 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE* 4.4 12.6 - - + -
50G ILE* 4.3 14.6 - - + -
96G ILE* 2.9 23.5 + - + +
97G VAL 4.0 1.1 - - - +
99G LEU* 1.3 80.5 - - - +
101G ARG* 1.3 57.7 + - - +
103G VAL* 4.4 3.1 - - - -
104G SER* 3.0 30.1 + - - -
114G PHE* 4.0 9.2 - - + -
116G CYS* 3.5 33.7 - - + -
139G ILE* 3.6 29.2 - - + -
142G PHE* 3.9 19.0 - - + +
143G PHE* 3.4 36.3 - - + -
158G PHE* 4.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 101 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G VAL* 3.0 39.9 + - - +
98G GLU* 3.9 11.1 - - - +
100G MET* 1.3 77.9 - - - +
102G ASP* 1.3 65.5 + - - +
104G SER* 2.5 23.4 + - - +
105G LYS* 3.1 32.4 + - + +
138G LYS* 4.8 8.5 - - - +
142G PHE* 3.4 32.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLU* 3.1 25.4 + - - +
99G LEU* 3.7 5.8 - - + +
101G ARG* 1.3 81.9 - - - +
103G VAL* 1.3 63.6 + - + +
105G LYS* 3.1 37.1 + - - +
106G GLU* 3.3 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G LEU* 3.9 15.5 - - + -
48G ILE* 4.2 12.3 - - + -
86G ARG* 4.1 17.5 - - - +
99G LEU* 2.8 42.3 + - + +
100G MET* 3.9 7.4 - - - +
102G ASP* 1.3 77.9 - - + +
104G SER* 1.3 59.2 + - - +
106G GLU* 3.1 15.8 + - - +
108G HIS* 2.8 25.6 + - + -
114G PHE* 3.6 35.0 - - + -
143G PHE* 4.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G MET 3.0 16.5 + - - -
101G ARG* 2.5 25.5 + - - +
103G VAL* 1.3 76.0 - - - +
105G LYS* 1.3 62.0 + - - +
106G GLU 3.2 4.8 + - - +
142G PHE* 3.4 36.6 + - - +
143G PHE* 3.7 17.7 - - - -
147G ARG 4.9 2.7 + - - +
148G CYS* 3.3 26.5 - - - +
150G SER* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ARG* 3.1 33.3 + - + +
102G ASP* 3.5 29.5 + - - +
103G VAL 3.1 1.0 - - - -
104G SER* 1.3 78.3 - - - +
106G GLU* 1.3 64.8 + - - +
----------------------------------------------------------
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