Contacts of the helix formed by residues 117 - 135 (chain G) in PDB entry 4KYI
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 ARG 117 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LYS 5.4 0.2 + - - -
103G LEU* 3.5 19.1 - - - +
104G LEU 4.2 9.3 + - - -
105G ASP* 3.2 31.8 + - + +
115G GLY 3.2 0.6 - - - -
116G ASP* 1.3 79.0 + - - +
118G PHE* 1.3 60.3 + - - +
119G ARG 3.2 1.1 - - - -
120G ASN* 3.0 8.8 + - - +
121G ILE* 2.9 40.5 + - + +
183G VAL* 4.6 8.5 - - - +
186G LEU* 3.4 47.5 + - + +
187G GLU* 3.4 34.8 + - - +
189G LEU* 4.7 2.2 - - + -
190G ASP* 3.5 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G MET* 3.5 36.6 - - + -
98G LEU* 5.2 1.8 - - + -
100G ILE* 4.7 12.6 - - + -
103G LEU* 3.9 34.6 + - + +
105G ASP* 4.0 2.0 + - - +
115G GLY* 3.6 10.1 + - - +
117G ARG* 1.3 80.7 - - - +
119G ARG* 1.3 59.7 + - - +
121G ILE* 3.4 8.1 + - + +
122G LEU* 3.3 42.9 + - + +
265G VAL* 4.6 4.7 - - + -
266G GLN* 3.9 27.8 - - + -
269G GLY* 4.6 13.5 - - - -
275G PHE* 4.5 24.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G GLY 3.3 14.5 + - - +
116G ASP* 3.6 28.2 - - - +
117G ARG 3.2 0.2 - - - -
118G PHE* 1.3 80.8 - - - +
120G ASN* 1.3 88.7 + - - +
122G LEU* 3.2 5.3 + - - -
123G ASP* 3.0 33.8 + - - +
193G LEU 4.5 0.2 + - - -
194G ASN* 3.9 13.5 - - - +
198G THR* 5.3 10.5 - - - +
212G ARG* 3.2 28.5 - - - +
262G ALA* 3.3 37.1 - - + +
263G GLN* 3.9 17.8 - - + +
266G GLN* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G ASP 2.4 25.9 + - - -
117G ARG* 3.0 9.6 + - - +
119G ARG* 1.3 104.1 + - - +
121G ILE* 1.3 63.6 + - - +
123G ASP* 3.5 4.4 + - - +
124G VAL* 3.2 27.2 + - - +
189G LEU* 3.7 12.3 - - + -
190G ASP* 3.8 25.5 + - - +
193G LEU* 3.5 32.8 - - + +
194G ASN* 4.1 6.5 - - - +
212G ARG* 4.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LEU* 4.1 27.1 - - + -
103G LEU* 3.6 24.9 - - + -
117G ARG* 2.9 23.0 + - + +
118G PHE* 3.6 9.6 - - + +
119G ARG 3.3 0.2 - - - -
120G ASN* 1.3 76.2 - - - +
122G LEU* 1.3 59.3 + - + +
124G VAL* 3.4 7.2 + - + +
125G ILE* 3.1 32.2 + - + +
176G ILE* 4.5 13.9 - - + -
179G LEU* 5.0 7.2 - - + -
180G THR* 4.5 4.7 - - + -
186G LEU* 3.8 22.2 - - + -
189G LEU* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G MET* 3.8 30.3 - - + -
81G ILE* 6.1 0.4 - - + -
98G LEU* 5.8 1.1 - - + -
118G PHE* 3.3 38.8 - - + +
119G ARG* 3.2 7.8 + - - +
121G ILE* 1.3 75.7 - - + +
123G ASP* 1.3 55.3 + - - +
125G ILE* 3.0 15.9 + - + +
126G TYR* 2.7 57.0 + - + +
262G ALA* 3.6 26.5 - - + +
265G VAL* 3.7 25.1 - - + -
266G GLN 4.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ARG* 3.0 20.8 + - - +
120G ASN* 3.7 13.9 - - - +
122G LEU* 1.3 74.3 - - - +
124G VAL* 1.3 56.7 + - - +
126G TYR* 3.5 8.2 + - - +
127G MET* 3.0 30.8 + - - +
159G TYR* 2.9 37.7 + - + -
193G LEU* 4.6 7.2 - - + +
212G ARG* 3.2 26.0 + - - -
213G LEU* 5.0 4.0 + - - +
260G SER* 4.1 5.9 + - - -
262G ALA* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ASN 3.2 14.3 + - - +
121G ILE* 3.4 11.0 - - + +
122G LEU 3.1 0.4 - - - -
123G ASP* 1.3 75.5 - - - +
125G ILE* 1.3 66.5 + - - +
127G MET* 3.3 11.9 + - + +
128G MET* 3.1 22.2 + - - +
159G TYR* 5.4 0.4 - - + -
163G LEU* 4.2 12.3 - - + -
170G ILE* 3.9 34.5 - - + -
176G ILE* 3.9 19.3 - - + -
179G LEU* 5.0 5.6 - - + -
189G LEU* 3.6 26.0 - - + -
193G LEU* 4.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G MET* 5.9 0.9 - - - -
81G ILE* 4.5 13.2 - - + -
84G VAL* 5.3 1.7 - - + +
86G MET* 3.7 27.1 - - + -
94G LEU* 3.8 32.8 - - + -
98G LEU* 4.5 12.8 - - + -
121G ILE* 3.1 21.0 + - + +
122G LEU* 3.0 19.2 + - + +
124G VAL* 1.3 75.1 - - - +
126G TYR* 1.3 70.3 + - + +
128G MET* 3.3 10.7 + - - +
129G GLN* 3.4 15.1 + - - +
176G ILE* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G SER* 2.9 42.8 + - - -
81G ILE* 4.9 2.9 - - + -
84G VAL* 4.4 17.2 - - + +
122G LEU* 2.7 42.5 + - + +
123G ASP* 3.8 8.1 - - - +
125G ILE* 1.3 83.4 - - + +
127G MET* 1.3 60.9 + - - +
130G MET* 3.2 37.1 + - - +
213G LEU* 3.8 15.3 - - + -
261G ILE* 3.6 28.7 - - + -
262G ALA* 3.4 33.2 - - + -
265G VAL* 3.3 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ASP 3.0 15.4 + - - +
124G VAL* 3.6 9.9 - - + +
126G TYR* 1.3 76.5 - - - +
128G MET* 1.3 65.7 + - - +
130G MET* 4.1 1.5 - - - -
131G LYS* 3.2 25.5 + - + +
156G ILE* 4.3 14.1 - - + +
159G TYR* 3.6 40.6 - - + -
160G GLU* 3.6 26.5 - - + +
163G LEU* 3.6 31.0 - - + -
170G ILE* 4.1 31.2 - - + +
213G LEU* 3.7 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G MET* 4.6 6.3 - - + -
90G ASP* 5.1 1.3 - - - +
124G VAL 3.1 16.3 + - - +
125G ILE 3.7 6.5 - - - +
126G TYR 3.2 0.4 - - - -
127G MET* 1.3 81.2 - - - +
129G GLN* 1.3 97.5 + - + +
131G LYS* 3.4 6.6 + - - +
132G LYS* 3.3 32.9 + - + +
170G ILE* 4.0 21.5 - - + +
171G ASN* 4.4 7.4 - - - -
172G ASN* 3.4 42.2 - - - +
173G VAL* 3.6 18.8 - - + +
176G ILE* 3.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G VAL* 3.8 19.7 - - + +
85G GLY 3.8 9.7 + - - -
86G MET* 3.7 32.0 - - + +
87G ASP* 4.3 5.2 - - - +
90G ASP* 4.0 10.1 + - - +
125G ILE 3.4 10.1 + - - +
128G MET* 1.3 97.9 - - + +
130G MET* 1.3 57.2 + - - +
131G LYS 3.3 0.9 - - - -
132G LYS* 3.7 23.6 + - - +
133G HIS* 2.4 66.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G VAL* 3.6 18.8 - - + +
126G TYR* 3.2 21.7 + - - +
127G MET* 4.4 2.5 - - - +
129G GLN* 1.3 76.7 - - - +
131G LYS* 1.3 61.4 + - - +
133G HIS* 3.8 1.3 + - - -
134G LEU* 3.4 25.3 + - - +
152G LEU* 4.4 7.6 - - + -
156G ILE* 4.1 8.2 - - + +
213G LEU* 3.7 34.5 - - + -
217G ASP* 3.8 28.3 - - + +
218G LEU* 4.3 15.9 - - + +
221G LEU* 3.8 33.4 - - + +
261G ILE* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G MET* 3.2 20.4 + - + +
128G MET* 3.7 6.7 - - - +
129G GLN 3.3 0.2 - - - -
130G MET* 1.3 76.2 - - - +
132G LYS* 1.3 59.6 + - + +
133G HIS 3.1 2.5 - - - -
134G LEU* 3.3 5.7 + - + +
135G GLU* 2.7 63.5 + - + +
153G LYS* 5.8 6.5 - - - +
156G ILE* 3.7 28.0 - - + -
160G GLU* 3.2 36.3 + - - +
170G ILE 5.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G ASP* 4.1 16.4 + - - -
128G MET* 3.3 25.4 + - + +
129G GLN* 3.7 32.2 + - - +
130G MET 3.4 0.4 - - - -
131G LYS* 1.3 77.7 - - + +
133G HIS* 1.3 61.1 + - + +
135G GLU* 4.0 19.0 + - - +
136G SER* 4.0 9.9 + - - -
171G ASN 5.2 9.0 - - - +
172G ASN* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G VAL 3.2 24.3 + - - -
85G GLY* 3.8 13.4 + - - -
129G GLN* 2.4 53.1 + - + +
130G MET* 4.1 4.1 - - - +
131G LYS 3.1 0.4 - - - -
132G LYS* 1.3 77.6 - - - +
134G LEU* 1.3 64.3 + - - +
135G GLU 3.1 1.8 - - - -
136G SER* 2.3 31.4 + - - -
137G VAL* 3.6 0.9 - - - +
221G LEU* 3.8 21.5 - - + +
225G LEU* 3.5 23.8 - - + +
232G LEU* 3.8 29.5 - - + +
233G ILE* 4.7 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G MET 3.4 11.0 + - - +
131G LYS* 3.3 9.6 + - + +
133G HIS* 1.3 78.1 - - - +
135G GLU* 1.3 56.7 + - - +
136G SER 3.0 5.8 + - - -
137G VAL* 3.2 23.1 + - + +
149G TYR* 4.0 27.1 + - + -
152G LEU* 3.7 30.5 - - + -
153G LYS* 3.9 28.9 - - + +
156G ILE* 3.6 28.3 - - + -
221G LEU* 4.5 4.4 - - + +
224G LEU* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G LYS* 2.7 51.6 + - + +
132G LYS* 4.1 16.8 - - - +
133G HIS 3.1 0.6 - - - -
134G LEU* 1.3 75.6 - - + +
136G SER* 1.3 57.1 - - - +
137G VAL 3.7 1.1 - - - -
153G LYS* 5.2 8.5 - - - +
----------------------------------------------------------
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