Contacts of the helix formed by residues 155 - 170 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H VAL* 3.5 38.6 - - + -
72H LEU* 4.2 28.7 - - + +
73H HIS* 4.4 16.2 - - + -
76H ALA* 4.2 18.2 - - + -
81H LEU* 2.7 20.3 + - + +
82H PHE* 4.7 7.2 - - + -
92H ILE* 4.1 6.3 - - + -
96H VAL* 4.1 20.9 - - + -
154H SER* 1.3 73.6 - - - +
156H ALA* 1.4 63.4 + - - +
158H VAL* 3.1 6.8 + - - +
159H ILE* 3.1 34.1 + - + +
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Residues in contact with ALA 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ILE* 3.7 9.9 - - + +
95H TYR* 3.7 34.5 - - + +
96H VAL* 3.5 17.1 - - + +
99H THR* 5.3 2.1 + - - -
148H LEU* 4.0 15.7 - - + +
149H VAL* 5.7 0.4 - - + -
154H SER* 3.1 10.1 + - - +
155H LEU* 1.4 79.1 - - - +
157H ASP* 1.3 56.3 + - - +
159H ILE* 3.5 1.4 + - - +
160H LEU* 3.0 31.5 + - - +
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Residues in contact with ASP 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PHE* 3.5 7.6 - - - +
148H LEU* 2.8 27.9 + - - +
152H GLN 3.5 5.0 - - - +
153H LEU* 3.2 25.9 - - + -
154H SER* 2.8 35.9 + - - +
156H ALA* 1.3 74.3 - - - +
158H VAL* 1.3 65.3 + - - +
160H LEU* 3.8 0.7 - - - +
161H LEU* 2.9 25.5 + - - +
184H TYR* 2.5 34.9 + - - +
188H LEU* 4.1 7.3 - - + +
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Residues in contact with VAL 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TRP* 3.8 48.8 - - + +
22H VAL* 4.2 14.1 - - + -
25H ALA* 4.3 19.7 - - + -
81H LEU* 5.1 5.6 - - + -
153H LEU* 4.5 13.7 - - + -
154H SER 3.3 16.8 - - - +
155H LEU* 3.1 9.0 + - - +
157H ASP* 1.3 78.8 - - - +
159H ILE* 1.3 58.3 + - + +
161H LEU* 3.6 5.5 - - - +
162H GLN* 2.9 27.9 + - - +
194H ILE* 5.7 4.5 - - + -
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Residues in contact with ILE 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H SER* 3.7 29.2 - - - -
22H VAL* 4.7 13.0 - - + -
72H LEU* 4.5 11.7 - - + -
96H VAL* 4.2 19.5 - - + -
99H THR* 4.0 20.9 - - + -
100H LEU* 4.0 24.5 - - + -
103H LEU* 4.8 0.2 - - + -
155H LEU* 3.1 20.3 + - + +
156H ALA* 4.0 3.6 - - - +
158H VAL* 1.3 79.4 - - + +
160H LEU* 1.3 64.0 + - - +
162H GLN* 3.2 9.6 + - - +
163H THR* 2.8 35.1 + - - +
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Residues in contact with LEU 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H THR* 4.1 17.6 - - + +
102H LEU* 6.1 1.3 - - + -
132H TYR* 6.3 0.2 - - + -
133H PHE* 4.6 8.5 - - + -
136H PHE* 3.8 49.1 - - + -
148H LEU* 3.9 13.0 - - + -
156H ALA 3.0 18.7 + - - +
157H ASP 3.8 3.6 - - - +
159H ILE* 1.3 78.1 - - - +
161H LEU* 1.3 65.3 + - - +
163H THR* 3.5 2.4 - - + -
164H ILE* 2.8 47.2 + - + +
181H LEU* 4.3 7.0 - - + -
184H TYR* 3.9 21.5 - - + +
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Residues in contact with LEU 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H TRP* 3.5 24.2 - - + -
157H ASP 2.9 17.9 + - - +
158H VAL* 3.6 5.6 - - - +
160H LEU* 1.3 76.4 - - - +
162H GLN* 1.3 65.1 + - - +
163H THR 3.2 0.2 + - - -
164H ILE* 3.2 5.9 + - + +
165H LEU* 2.9 52.2 + - + +
184H TYR* 5.2 1.5 - - + -
185H THR* 3.9 30.7 - - + +
188H LEU* 4.0 26.0 - - + -
189H SER* 4.0 9.9 - - - +
194H ILE* 4.0 21.1 - - + -
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Residues in contact with GLN 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 3.6 25.3 - - - +
18H SER* 2.8 38.7 + - - +
21H TRP* 3.8 40.2 + - + +
103H LEU* 3.7 23.5 - - + +
158H VAL 2.9 16.9 + - - +
159H ILE* 3.3 13.5 - - - +
161H LEU* 1.3 77.9 - - - +
163H THR* 1.3 65.8 + - - +
165H LEU* 3.5 3.3 + - - +
166H ALA* 3.1 21.9 + - + +
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Residues in contact with THR 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H THR* 3.4 19.8 - - + +
102H LEU* 4.0 21.8 - - + -
103H LEU* 3.7 34.1 - - + +
106H LEU* 4.6 1.1 - - + -
159H ILE* 2.8 20.3 + - - +
160H LEU* 3.5 4.5 - - + -
162H GLN* 1.3 76.9 - - - +
164H ILE* 1.3 62.0 + - + +
166H ALA* 3.1 7.1 + - - +
167H LEU* 2.7 46.6 + - + +
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Residues in contact with ILE 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H PHE* 3.9 25.1 - - + -
160H LEU* 2.8 42.7 + - + +
161H LEU* 3.6 6.3 - - - +
163H THR* 1.3 76.3 - - - +
165H LEU* 1.3 68.1 + - + +
167H LEU* 3.1 10.6 + - - +
168H GLU* 2.8 37.5 + - + +
174H ILE* 4.8 0.2 - - - +
175H LEU* 3.9 26.2 - - + -
181H LEU* 4.3 17.3 - - + -
184H TYR* 5.0 2.7 - - + -
185H THR* 3.8 22.0 - - + +
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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
----------------------------------------------------------
21H TRP* 3.8 25.6 - - + -
161H LEU* 2.9 30.1 + - + +
162H GLN 3.8 3.6 - - - +
164H ILE* 1.3 78.7 - - + +
166H ALA* 1.3 59.1 + - - +
168H GLU* 3.0 23.0 + - - +
169H GLU* 2.8 32.5 + - + +
185H THR* 4.1 24.0 - - + -
189H SER* 5.2 2.9 - - - +
198H LEU* 4.3 17.3 - - + -
204H LYS* 5.8 2.0 - - - -
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Residues in contact with ALA 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ARG* 5.2 5.8 - - - +
103H LEU* 4.8 4.7 - - + -
106H LEU* 3.5 23.5 - - + +
162H GLN* 3.1 14.2 + - + +
163H THR* 3.1 11.9 - - - +
165H LEU* 1.3 77.8 - - - +
167H LEU* 1.3 64.9 + - - +
169H GLU* 3.1 32.1 + - - +
170H LYS* 3.6 9.4 + - - +
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Residues in contact with LEU 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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102H LEU* 3.9 16.2 - - + -
106H LEU* 3.8 13.7 - - + -
124H MET* 3.8 41.5 - - + +
128H ALA* 4.4 4.5 - - + -
133H PHE* 3.9 25.8 - - + -
163H THR* 2.7 33.6 + - + +
164H ILE* 3.4 5.2 - - - +
166H ALA* 1.3 80.1 - - - +
168H GLU* 1.3 50.8 + - - +
170H LYS* 2.7 8.8 + - - +
171H ILE* 2.7 42.8 + - + +
174H ILE* 4.5 12.1 - - + -
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Residues in contact with GLU 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H ILE* 2.8 30.8 + - + +
165H LEU* 3.0 21.2 + - - +
167H LEU* 1.3 72.9 - - - +
169H GLU* 1.3 67.8 + - - +
171H ILE 3.5 10.3 - - - +
172H PRO* 3.2 35.7 - - + +
174H ILE* 3.8 12.9 - - + +
175H LEU* 3.8 26.6 - - - +
185H THR* 5.5 2.7 - - - +
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Residues in contact with GLU 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ARG* 3.0 43.6 + - - -
165H LEU* 2.8 20.8 + - - +
166H ALA* 3.4 15.2 - - - +
167H LEU 3.0 0.6 - - - -
168H GLU* 1.3 80.7 - - - +
170H LYS* 1.3 68.6 + - + +
172H PRO* 4.9 3.1 - - - +
204H LYS* 4.5 3.5 + - - -
207H PRO* 3.4 19.3 - - + +
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Residues in contact with LYS 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU* 4.2 20.8 + - + +
109H HIS* 2.6 45.8 + - + +
110H PRO* 5.2 3.4 - - - +
121H VAL* 4.7 16.1 - - + +
124H MET* 4.6 9.2 - - + -
166H ALA 4.1 10.1 - - - +
167H LEU 2.7 8.1 + - - +
169H GLU* 1.3 91.6 - - + +
171H ILE* 1.3 68.5 + - + +
172H PRO* 3.2 9.1 - - - +
207H PRO* 6.0 5.2 - - - -
208H PRO* 6.1 4.1 - - - +
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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