Contacts of the helix formed by residues 155 - 170 (chain G) in PDB entry 1GUM
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 LEU 155 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL* 3.5 38.4 - - + -
72G LEU* 4.2 28.7 - - + +
73G HIS* 4.4 15.5 - - + -
76G ALA* 4.2 17.7 - - + -
81G LEU* 2.7 19.0 + - + +
82G PHE* 4.7 7.9 - - + -
92G ILE* 4.1 7.0 - - + -
96G VAL* 4.1 20.9 - - + -
154G SER* 1.3 74.2 - - - +
156G ALA* 1.4 63.6 + - - +
158G VAL* 3.1 6.7 + - - +
159G ILE* 3.1 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ILE* 3.7 10.3 - - + +
95G TYR* 3.7 33.6 - - + +
96G VAL* 3.5 16.8 - - + +
99G THR* 5.3 2.1 + - - -
148G LEU* 4.0 15.2 - - + +
149G VAL* 5.7 0.4 - - + -
154G SER* 3.1 10.3 + - - +
155G LEU* 1.4 78.7 - - - +
157G ASP* 1.3 56.1 + - - +
159G ILE* 3.5 1.4 + - - +
160G LEU* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G PHE* 3.5 7.9 - - - +
148G LEU* 2.8 28.9 + - - +
152G GLN 3.5 5.2 - - - +
153G LEU* 3.2 25.9 - - + -
154G SER* 2.8 35.0 + - - +
156G ALA* 1.3 75.4 - - - +
158G VAL* 1.3 65.4 + - - +
160G LEU* 3.8 0.7 - - - +
161G LEU* 2.9 25.5 + - - +
184G TYR* 2.5 33.6 + - - +
188G LEU* 4.1 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G TRP* 3.8 48.0 - - + +
22G VAL* 4.2 14.6 - - + -
25G ALA* 4.3 18.6 - - + -
81G LEU* 5.1 6.1 - - + -
153G LEU* 4.5 14.4 - - + -
154G SER 3.3 17.0 - - - +
155G LEU* 3.1 7.7 + - - +
157G ASP* 1.3 78.5 - - - +
159G ILE* 1.3 59.8 + - + +
161G LEU* 3.6 6.1 - - - +
162G GLN* 2.9 27.9 + - - +
194G ILE* 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER* 3.7 29.4 - - - -
21G TRP* 5.6 0.2 - - + -
22G VAL* 4.7 12.8 - - + -
72G LEU* 4.5 11.7 - - + -
96G VAL* 4.2 20.2 - - + -
99G THR* 4.0 21.1 - - + -
100G LEU* 4.0 24.5 - - + -
103G LEU* 4.8 0.2 - - + -
155G LEU* 3.1 21.2 + - + +
156G ALA* 4.0 3.6 - - - +
158G VAL* 1.3 79.6 - - + +
160G LEU* 1.3 63.7 + - - +
162G GLN* 3.2 9.1 + - - +
163G THR* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G THR* 4.1 17.4 - - + +
102G LEU* 6.1 1.3 - - + -
133G PHE* 4.6 7.4 - - + -
136G PHE* 3.8 50.0 - - + -
148G LEU* 3.9 13.0 - - + -
156G ALA 3.0 19.1 + - - +
157G ASP 3.8 3.6 - - - +
159G ILE* 1.3 79.6 - - - +
161G LEU* 1.3 62.2 + - - +
163G THR* 3.5 2.4 - - + -
164G ILE* 2.8 48.7 + - + +
181G LEU* 4.3 6.5 - - + -
184G TYR* 3.9 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G TRP* 3.5 24.7 - - + -
157G ASP 2.9 18.1 + - - +
158G VAL* 3.6 6.3 - - - +
160G LEU* 1.3 77.7 - - - +
162G GLN* 1.3 64.0 + - - +
163G THR 3.2 0.3 + - - -
164G ILE* 3.2 5.6 + - + +
165G LEU* 2.9 51.8 + - + +
184G TYR* 5.2 1.5 - - + -
185G THR* 3.9 31.0 - - + +
188G LEU* 4.0 26.0 - - + -
189G SER* 4.0 9.9 - - - +
194G ILE* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 3.6 26.2 - - - +
18G SER* 2.8 38.6 + - - +
21G TRP* 3.8 39.8 - - + +
103G LEU* 3.7 23.3 - - + +
158G VAL 2.9 17.7 + - - +
159G ILE* 3.3 12.5 - - - +
161G LEU* 1.3 77.6 - - - +
163G THR* 1.3 67.1 + - - +
165G LEU* 3.5 2.8 + - - +
166G ALA* 3.1 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G THR* 3.4 19.4 - - + +
102G LEU* 4.0 22.4 - - + -
103G LEU* 3.7 32.4 - - + +
106G LEU* 4.6 1.1 - - + -
133G PHE* 5.9 0.2 - - + -
159G ILE* 2.8 20.2 + - - +
160G LEU* 3.5 5.2 - - + -
162G GLN* 1.3 76.2 - - - +
164G ILE* 1.3 61.9 + - + +
166G ALA* 3.1 7.2 + - - +
167G LEU* 2.7 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G PHE* 3.9 25.6 - - + -
160G LEU* 2.8 43.5 + - + +
161G LEU* 3.6 6.3 - - - +
163G THR* 1.3 76.7 - - - +
165G LEU* 1.3 68.5 + - + +
167G LEU* 3.1 9.9 + - - +
168G GLU* 2.8 37.1 + - + +
174G ILE* 4.8 0.6 - - + +
175G LEU* 3.9 26.9 - - + -
181G LEU* 4.3 17.5 - - + -
184G TYR* 5.0 2.7 - - + -
185G THR* 3.8 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G TRP* 3.8 25.8 - - + -
161G LEU* 2.9 30.3 + - + +
162G GLN 3.8 3.1 - - - +
164G ILE* 1.3 80.5 - - + +
166G ALA* 1.3 59.9 + - - +
168G GLU* 3.0 22.2 + - - +
169G GLU* 2.8 31.9 + - + +
185G THR* 4.1 24.0 - - + -
189G SER* 5.2 2.5 - - - +
198G LEU* 4.3 17.0 - - + -
204G LYS* 5.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ARG* 5.3 5.8 - - - +
103G LEU* 4.8 4.7 - - + -
106G LEU* 3.5 23.9 - - + +
162G GLN* 3.1 13.9 + - + +
163G THR* 3.1 12.3 - - - +
165G LEU* 1.3 77.0 - - - +
167G LEU* 1.3 66.3 + - - +
169G GLU* 3.1 32.3 + - - +
170G LYS* 3.6 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 3.9 16.2 - - + -
106G LEU* 3.8 13.9 - - + -
124G MET* 3.8 42.4 - - + +
128G ALA* 4.4 5.2 - - + -
133G PHE* 3.9 25.8 - - + -
163G THR* 2.7 33.0 + - + +
164G ILE 3.4 4.0 - - - +
166G ALA* 1.3 79.7 - - - +
168G GLU* 1.3 50.8 + - - +
170G LYS* 2.7 8.8 + - - +
171G ILE* 2.7 43.8 + - + +
174G ILE* 4.5 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164G ILE* 2.8 30.8 + - + +
165G LEU* 3.0 20.8 + - - +
167G LEU* 1.3 73.2 - - - +
169G GLU* 1.3 67.7 + - - +
170G LYS 3.0 0.2 - - - -
171G ILE 3.5 10.5 - - - +
172G PRO* 3.2 36.4 - - + +
174G ILE* 3.8 12.9 - - + +
175G LEU* 3.8 28.2 - - - +
185G THR* 5.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ARG* 3.0 42.9 + - - -
165G LEU* 2.8 21.1 + - + +
166G ALA* 3.4 15.9 - - - +
167G LEU 3.0 0.4 - - - -
168G GLU* 1.3 81.1 - - - +
170G LYS* 1.3 68.3 + - + +
172G PRO* 4.9 3.1 - - - +
204G LYS* 4.5 4.2 + - - -
207G PRO* 3.4 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F VAL* 6.0 0.5 - - - +
106G LEU* 4.2 19.6 + - + +
109G HIS* 2.7 46.3 + - + +
110G PRO* 5.2 3.8 - - - +
121G VAL* 4.7 16.2 - - + +
124G MET* 4.6 9.2 - - + -
166G ALA 4.1 10.3 - - - +
167G LEU 2.7 7.3 + - - +
169G GLU* 1.3 91.0 - - + +
171G ILE* 1.3 68.6 + - + +
172G PRO* 3.2 9.6 - - - +
207G PRO* 6.0 4.5 - - - -
208G PRO* 6.1 3.4 - - - +
----------------------------------------------------------
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