Contacts of the helix formed by residues 155 - 169 (chain H) in PDB entry 4GTU
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 VAL 155 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ARG 5.0 1.3 - - - +
96H VAL* 3.8 32.1 - - + +
99H LEU* 3.6 28.3 - - + +
100H GLU* 4.7 6.5 - - + +
147H PHE* 4.7 1.3 - - + -
148H VAL* 4.6 11.9 - - + -
153H THR* 3.1 19.1 - - - +
154H PHE* 1.3 98.8 - - + +
156H ASP* 1.3 69.3 + - - +
158H LEU* 2.9 9.6 + - + +
159H ALA* 2.8 32.6 + - - +
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Residues in contact with ASP 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H TRP* 2.9 45.5 - - + +
147H PHE* 3.5 6.9 + - - -
148H VAL* 4.5 1.7 - - - +
151H LYS 3.8 0.9 - - - +
152H ILE* 3.4 8.9 - - + -
153H THR* 2.9 40.5 + - - +
154H PHE 3.1 0.2 - - - -
155H VAL* 1.3 86.1 - - - +
157H PHE* 1.3 60.1 + - + +
159H ALA* 4.5 1.8 - - - -
160H TYR* 3.1 26.5 + - - +
183H PHE* 3.1 28.4 - - + -
187H PHE* 4.5 6.5 - - + -
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Residues in contact with PHE 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ALA* 4.3 17.8 - - + +
18H LEU* 3.5 31.3 - - + +
19H LEU* 3.6 35.2 - - + -
22H TYR* 3.8 33.4 - + + -
76H LEU* 5.2 2.5 - - + -
85H LEU* 5.0 2.0 - - + -
152H ILE* 4.4 9.4 - - + -
153H THR 3.3 23.6 - - - -
154H PHE* 3.3 12.6 - - - +
155H VAL 3.0 0.4 - - - -
156H ASP* 1.3 78.4 - - - +
158H LEU* 1.3 65.4 + - - +
160H TYR* 3.3 4.7 + - - +
161H ASP* 3.0 22.5 + - - +
187H PHE* 3.4 38.1 - + - -
193H ILE* 4.8 0.4 - - + -
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ALA* 4.3 16.1 - - + +
73H ASN* 3.5 23.6 - - - +
76H LEU* 4.1 17.7 - - + -
99H LEU* 5.5 0.7 - - + +
100H GLU* 3.8 31.2 - - + +
103H ALA* 4.4 20.2 - - + +
104H MET* 5.0 6.5 - - + +
154H PHE* 3.4 10.2 + - + +
155H VAL* 2.9 11.7 + - + +
157H PHE* 1.3 78.9 - - - +
159H ALA* 1.3 63.6 + - - +
161H ASP* 3.0 22.4 + - + +
162H VAL* 3.1 18.8 + - + +
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Residues in contact with ALA 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H LEU* 4.4 13.2 - - + -
103H ALA* 4.6 6.1 - - - +
137H PHE* 6.1 1.8 - - + -
147H PHE* 3.8 35.7 - - + -
155H VAL 2.8 19.7 + - - +
156H ASP* 4.0 4.5 - - - +
158H LEU* 1.3 72.3 - - - +
160H TYR* 1.3 62.3 + - - +
162H VAL* 3.4 8.2 + - - +
163H LEU* 3.1 29.5 + - + +
183H PHE* 4.5 3.4 - - + -
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Residues in contact with TYR 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H HIS* 5.3 5.8 - + - -
18H LEU* 4.2 13.9 - - + -
156H ASP 3.1 21.7 + - - +
157H PHE 3.6 4.3 - - - +
158H LEU 3.2 0.2 - - - -
159H ALA* 1.3 75.5 - - - +
161H ASP* 1.3 60.8 + - - +
163H LEU* 3.3 4.5 + - - +
164H ASP* 2.8 52.2 + - + +
167H ARG* 3.7 13.2 + - - -
183H PHE* 4.2 8.7 - + + -
184H ILE* 3.5 37.9 - - + -
187H PHE* 3.6 46.4 - + + -
188H GLU* 2.9 22.2 + - + +
197H MET* 5.0 6.9 - - + +
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Residues in contact with ASP 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ARG* 3.5 14.5 + - - +
11H GLY 4.5 8.4 - - - +
12H LEU* 5.2 2.8 - - - +
14H HIS* 3.3 29.7 - - + +
15H ALA* 4.5 17.9 + - + +
107H SER* 4.8 5.2 + - - -
157H PHE 3.0 13.1 + - - +
158H LEU* 3.0 17.5 + - + +
160H TYR* 1.3 79.9 - - - +
162H VAL* 1.3 63.1 + - + +
164H ASP* 3.2 6.4 + - - +
165H LEU* 3.0 38.3 + - - +
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Residues in contact with VAL 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ALA* 3.4 28.3 - - + +
106H VAL* 3.3 23.6 - - + -
107H SER* 3.1 24.9 - - - +
134H MET* 6.2 0.7 - - + -
137H PHE* 4.7 11.2 - - + -
158H LEU* 3.1 16.6 + - + +
159H ALA* 3.7 7.0 - - - +
160H TYR 3.3 0.2 - - - -
161H ASP* 1.3 76.9 - - + +
163H LEU* 1.3 61.0 + - + +
165H LEU* 3.3 3.2 + - - +
166H HIS* 3.0 47.5 + - + +
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Residues in contact with LEU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H MET* 4.2 30.0 - - + +
137H PHE* 4.9 9.9 - - + -
147H PHE* 5.2 5.4 - - + -
159H ALA* 3.1 19.3 + - + +
160H TYR* 3.8 3.6 - - - +
162H VAL* 1.3 83.8 - - + +
164H ASP* 1.3 57.8 + - - +
166H HIS* 4.1 3.5 - - - +
167H ARG* 2.9 36.1 + - - +
174H LEU* 4.6 4.5 - - + +
180H LEU* 4.2 29.6 - - + +
183H PHE* 4.1 18.8 - - + -
184H ILE* 3.8 31.9 - - + -
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Residues in contact with ASP 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ARG* 2.7 29.5 + - - +
14H HIS* 4.4 4.7 + - - -
160H TYR* 2.8 43.2 + - + +
161H ASP* 3.2 6.3 + - - +
163H LEU* 1.3 74.7 - - - +
165H LEU* 1.3 64.4 + - - +
167H ARG* 2.7 51.3 + - - +
168H ILE* 3.2 18.8 + - - +
184H ILE* 4.9 1.0 - - - +
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Residues in contact with LEU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ARG* 3.9 27.8 - - - +
11H GLY 6.1 0.4 - - - +
107H SER* 3.7 30.1 - - - +
110H LEU* 4.4 10.4 - - + +
161H ASP* 3.0 27.1 + - - +
162H VAL* 3.7 3.6 - - - +
164H ASP* 1.3 77.0 - - - +
166H HIS* 1.3 61.8 + - - +
168H ILE* 3.2 7.3 + - - +
169H PHE* 3.0 28.0 + - - +
207H LEU* 4.0 19.7 - - + +
208H TYR* 4.0 28.9 - - + +
214H TRP* 5.1 4.5 - - + -
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Residues in contact with HIS 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H VAL* 4.1 10.8 + - - +
107H SER* 5.0 2.5 - - - -
110H LEU* 3.6 28.6 - - + +
126H TYR* 2.7 26.9 + + - -
130H LEU* 3.4 28.1 - - + +
133H MET* 4.2 5.0 - - - -
134H MET* 4.1 26.5 - - + -
137H PHE* 6.3 0.6 - + - -
162H VAL* 3.0 33.7 + - + +
163H LEU 4.1 2.9 - - - +
165H LEU* 1.3 82.4 - - + +
167H ARG* 1.3 53.6 + - - +
169H PHE* 3.1 8.7 + + + +
170H GLU* 2.7 37.8 + - - +
173H CYS* 3.9 5.5 - - - -
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Residues in contact with ARG 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H TYR* 3.7 11.3 + - - -
163H LEU 2.9 13.4 + - - +
164H ASP* 2.7 56.0 + - - +
166H HIS* 1.3 76.9 - - - +
168H ILE* 1.3 71.6 + - + +
170H GLU 3.9 7.6 - - - -
171H PRO* 2.9 37.1 - - + +
173H CYS* 4.6 2.9 - - - -
174H LEU* 3.7 24.7 - - + +
184H ILE* 3.4 37.6 - - - +
188H GLU* 4.2 3.8 + - - -
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Residues in contact with ILE 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ARG* 5.0 8.7 - - - +
164H ASP* 3.2 32.0 + - - +
165H LEU* 3.2 6.5 + - - +
167H ARG* 1.3 92.4 - - + +
169H PHE* 1.3 60.5 + - - +
171H PRO* 4.7 4.8 - - - +
204H PRO* 6.3 0.7 - - + -
205H LYS* 4.3 23.6 - - - +
207H LEU* 5.4 15.3 - - + -
214H TRP* 4.3 16.9 - - + -
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Residues in contact with PHE 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H LEU* 4.0 28.5 - - + -
113H VAL* 5.1 2.2 - - + -
114H CYS* 4.0 9.9 - - - -
119H PHE* 3.8 25.6 - + - -
123H LYS* 3.3 48.2 + - + -
126H TYR* 4.1 20.6 - + - -
127H LEU* 5.0 7.0 - - + -
130H LEU* 5.2 4.5 - - + -
165H LEU 3.0 12.7 + - - +
166H HIS* 3.1 12.8 + + - +
168H ILE* 1.3 80.6 - - - +
170H GLU* 1.3 68.7 + - + +
171H PRO* 3.8 5.2 - - - +
214H TRP* 3.6 31.7 - + + -
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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) + - + + + + + -
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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