Contacts of the helix formed by residues 155 - 170 (chain A) in PDB entry 1GUL
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.6 35.4 - - + -
72A LEU* 4.2 26.7 - - + +
73A HIS* 4.5 13.2 - - + -
76A ALA* 4.0 20.9 - - + -
81A LEU* 2.7 22.9 + - + +
82A PHE* 4.8 7.9 - - + -
92A ILE* 4.2 6.3 - - + -
96A VAL* 3.9 20.4 - - + -
154A SER* 1.3 75.8 - - - +
156A ALA* 1.3 62.4 + - - +
158A VAL* 3.2 5.3 + - - -
159A ILE* 3.2 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.9 13.4 - - + +
95A TYR* 3.8 30.2 - - + +
96A VAL* 3.7 16.7 - - + +
99A THR* 5.3 1.7 + - - -
148A LEU* 4.1 14.9 - - + +
154A SER* 3.0 11.3 + - - +
155A LEU* 1.3 79.1 - - - +
157A ASP* 1.3 62.0 + - - +
159A ILE* 3.5 1.8 + - - +
160A LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A PHE* 3.6 9.7 - - - +
148A LEU* 2.8 29.3 + - - +
152A GLN 3.5 5.7 - - - +
153A LEU* 3.3 23.2 - - + -
154A SER* 2.9 32.6 + - - +
156A ALA* 1.3 76.1 - - - +
158A VAL* 1.3 59.1 + - - +
160A LEU* 3.9 0.3 - - - +
161A LEU* 2.8 30.8 + - - +
184A TYR* 2.6 31.9 + - - +
188A LEU* 3.9 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.5 49.3 - - + +
22A VAL* 4.1 15.0 - - + +
25A ALA* 4.0 20.4 - - + -
81A LEU* 5.2 6.5 - - + -
153A LEU* 4.6 14.1 - - + -
154A SER 3.6 13.2 - - - +
155A LEU* 3.2 8.8 + - - +
157A ASP* 1.3 79.7 - - - +
159A ILE* 1.3 54.2 + - + +
161A LEU* 3.5 6.3 - - + +
162A GLN* 2.7 33.4 + - - +
194A ILE* 5.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.8 28.5 - - - +
22A VAL* 4.4 7.6 - - + -
72A LEU* 4.3 8.5 - - + -
96A VAL* 4.5 14.6 - - + +
99A THR* 3.8 21.8 - - + -
100A LEU* 3.9 23.6 - - + -
103A LEU* 4.8 0.4 - - + -
155A LEU* 3.2 37.5 + - + +
156A ALA 4.1 2.5 - - - +
158A VAL* 1.3 78.8 - - + +
160A LEU* 1.3 55.6 + - - +
162A GLN* 3.3 10.1 + - - +
163A THR* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 4.1 18.1 - - + +
102A LEU* 6.0 1.3 - - + -
133A PHE* 4.6 8.1 - - + -
136A PHE* 3.8 49.1 - - + -
148A LEU* 3.8 18.6 - - + -
156A ALA 3.0 18.3 + - - +
157A ASP 3.9 2.9 - - - +
159A ILE* 1.3 75.5 - - - +
161A LEU* 1.3 65.8 + - - +
163A THR* 3.1 4.1 + - + -
164A ILE* 2.8 49.7 + - + +
181A LEU* 4.6 4.3 - - + -
184A TYR* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.4 28.9 - - + -
157A ASP 2.8 18.7 + - - +
158A VAL* 3.5 5.4 - - - +
160A LEU* 1.3 77.6 - - - +
162A GLN* 1.3 65.4 + - - +
164A ILE* 3.7 6.5 - - + +
165A LEU* 3.0 47.2 + - + +
184A TYR* 5.5 0.7 - - - -
185A THR* 4.0 23.6 - - + +
188A LEU* 4.0 24.1 - - + +
189A SER* 4.0 15.9 - - - +
194A ILE* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.8 22.2 - - - +
18A SER* 2.7 41.3 + - - +
21A TRP* 3.7 40.6 - - + +
103A LEU* 3.8 22.0 - - + +
158A VAL 2.7 21.2 + - - +
159A ILE* 3.5 12.4 - - - +
160A LEU 3.2 0.2 - - - -
161A LEU* 1.3 73.5 - - - +
163A THR* 1.3 61.9 + - - +
165A LEU* 3.6 2.9 + - - +
166A ALA* 3.1 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 3.4 18.3 - - + +
102A LEU* 4.0 32.1 - - + -
103A LEU* 3.8 29.8 - - + +
106A LEU* 4.8 1.8 - - + -
133A PHE* 5.8 0.2 - - + -
159A ILE* 2.6 24.8 + - - +
160A LEU* 3.5 5.6 - - + -
162A GLN* 1.3 77.8 - - - +
164A ILE* 1.3 67.1 + - - +
166A ALA* 3.1 6.5 + - - +
167A LEU* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 3.8 26.0 - - + -
160A LEU* 2.8 40.2 + - + +
161A LEU* 3.7 5.8 - - - +
163A THR* 1.3 76.5 - - - +
165A LEU* 1.3 69.8 + - + +
167A LEU* 3.0 11.4 + - - +
168A GLU* 2.7 37.7 + - + +
174A ILE* 5.7 0.2 - - + -
175A LEU* 4.2 25.4 - - + -
181A LEU* 4.4 16.8 - - + -
184A TYR* 4.9 3.4 - - + -
185A THR* 3.9 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TRP* 3.8 31.2 - - + -
161A LEU* 3.0 24.4 + - + +
162A GLN* 3.8 3.8 - - - +
164A ILE* 1.3 81.9 - - + +
166A ALA* 1.3 62.2 + - - +
168A GLU* 3.3 22.5 + - - +
169A GLU* 3.1 27.1 + - - +
185A THR* 4.1 22.9 - - + -
189A SER* 5.1 3.1 - - - +
198A LEU* 4.1 19.3 - - + -
204A LYS* 5.6 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 4.9 7.4 - - - +
103A LEU* 5.0 5.4 - - + -
106A LEU* 4.1 22.8 - - + +
162A GLN* 3.1 15.6 + - + +
163A THR* 3.1 11.9 + - - +
165A LEU* 1.3 75.2 - - - +
167A LEU* 1.3 66.7 + - - +
169A GLU* 3.2 32.4 + - - +
170A LYS* 3.7 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.1 14.8 - - + -
106A LEU* 3.9 20.6 - - + -
124A MET* 3.9 35.2 - - + +
128A ALA* 4.3 4.5 - - + -
133A PHE* 3.8 25.8 - - + -
163A THR* 2.9 31.9 + - + +
164A ILE* 3.3 6.3 - - - +
166A ALA* 1.3 77.1 - - - +
168A GLU* 1.3 53.4 + - - +
170A LYS* 2.6 27.4 + - - +
171A ILE* 2.7 20.3 + - + +
174A ILE* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 2.7 28.3 + - + +
165A LEU* 3.7 24.3 - - - +
166A ALA 3.2 0.2 - - - -
167A LEU* 1.3 79.6 - - - +
169A GLU* 1.3 63.4 + - - +
170A LYS 3.0 0.6 + - - -
171A ILE 3.5 8.7 - - - +
172A PRO* 3.3 36.3 - - + +
174A ILE* 3.7 16.4 - - + -
175A LEU* 3.8 26.8 + - - +
185A THR* 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ARG* 2.8 45.1 + - - -
165A LEU* 3.1 21.7 + - - +
166A ALA* 3.4 14.0 - - - +
167A LEU 2.9 1.0 - - - -
168A GLU* 1.3 81.5 - - - +
170A LYS* 1.3 63.9 + - + +
172A PRO* 4.8 3.5 - - - +
204A LYS* 4.6 3.6 + - - -
207A PRO* 3.9 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 4.2 24.4 + - + -
109A HIS* 2.7 36.9 + - + +
110A PRO* 5.5 1.8 - - - +
121A VAL* 4.4 25.9 - - + +
124A MET* 4.5 6.7 - - + -
166A ALA 4.0 9.9 - - - +
167A LEU* 2.6 12.7 + - - +
169A GLU* 1.3 81.5 - - + +
171A ILE* 1.3 69.4 + - + +
172A PRO* 3.3 8.4 - - - +
208A PRO* 6.3 0.6 - - - +
----------------------------------------------------------
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