Contacts of the helix formed by residues 141 - 155 (chain g) in PDB entry 5GJQ
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 TYR 141 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9g THR* 5.0 2.5 + - - +
10g SER* 3.3 9.1 + - - +
140g GLY* 1.3 72.0 - - - -
142g GLY* 1.3 61.3 + - - +
143g ALA 3.0 0.2 - - - -
144g TYR* 2.9 30.0 + + - +
145g LEU* 2.8 44.2 + - + +
176g LEU* 4.2 2.7 - - + -
180g ASP* 3.4 30.5 - - + -
22o THR 4.9 1.4 + - - -
24o SER* 3.4 43.1 + - - -
25o TYR* 3.2 29.8 + + + +
132p LEU* 5.0 8.3 - - + -
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Residues in contact with GLY 142 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10g SER* 3.0 12.5 + - - -
12g LEU* 5.0 0.4 - - - -
138g ALA* 3.2 14.5 - - - +
139g THR 3.1 7.2 + - - -
140g GLY 3.0 1.6 - - - -
141g TYR* 1.3 80.1 - - - +
143g ALA* 1.3 57.2 + - - +
146g ALA* 2.8 26.9 + - - -
147g GLN 2.9 12.8 + - - -
176g LEU* 3.8 17.2 - - - +
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Residues in contact with ALA 143 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34f SER* 4.8 11.3 + - - +
36f HIS* 6.0 6.3 - - + +
138g ALA* 3.4 24.4 + - - +
139g THR 4.6 1.3 - - - -
140g GLY 2.9 16.7 + - - +
142g GLY* 1.3 77.5 - - - +
144g TYR* 1.3 69.2 + - + +
147g GLN* 3.8 17.8 - - + +
148g PRO* 4.4 2.3 - - - +
151g ARG* 5.8 0.5 + - - -
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Residues in contact with TYR 144 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33f PHE* 5.8 6.1 - - + -
34f SER* 3.2 27.4 + - - -
140g GLY 3.8 14.1 - - - -
141g TYR* 2.9 35.9 + + - +
143g ALA* 1.3 84.8 - - + +
145g LEU* 1.3 58.4 + - - +
148g PRO* 3.6 13.5 - - - +
132p LEU* 3.6 24.3 - - + -
133p ALA* 3.5 22.7 + - - +
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Residues in contact with LEU 145 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141g TYR* 2.8 29.2 + - + +
144g TYR* 1.3 80.8 - - - +
146g ALA* 1.3 62.7 + - - +
147g GLN 3.5 0.2 - - - -
148g PRO* 3.5 5.7 - - - +
149g LEU* 4.1 4.7 - - - +
175g VAL* 4.4 15.5 - - + -
176g LEU* 3.8 24.2 - - + -
179g ARG* 4.0 40.8 - - + +
180g ASP* 4.6 1.3 - - + +
25o TYR* 4.5 2.9 - - + -
132p LEU* 3.6 42.6 - - + +
135p MET* 4.8 1.3 - - + -
136p ALA* 3.2 29.0 - - - +
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Residues in contact with ALA 146 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12g LEU* 3.5 32.1 - - + -
142g GLY* 2.8 17.2 + - - +
145g LEU* 1.3 76.9 - - - +
147g GLN* 1.3 67.4 + - - +
149g LEU* 3.0 19.2 + - - +
150g LEU* 3.0 15.6 + - + +
172g CYS* 3.8 24.0 - - + +
175g VAL* 5.8 0.7 - - - -
176g LEU* 4.8 6.3 - - + -
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Residues in contact with GLN 147 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36f HIS 4.6 6.7 + - - -
132g TYR* 5.9 0.4 + - - -
134g ALA* 5.8 0.2 - - - +
136g SER* 3.2 48.9 + - - -
137g LEU* 3.8 11.1 + - - +
138g ALA* 4.2 4.5 - - + -
142g GLY 2.9 13.6 + - - +
143g ALA* 3.8 17.3 - - + +
146g ALA* 1.3 77.6 - - - +
148g PRO* 1.3 61.9 - - + +
150g LEU* 3.8 8.8 - - - +
151g ARG* 2.9 68.5 + - - +
165p ASN* 4.6 0.7 - - - -
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Residues in contact with PRO 148 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143g ALA 4.4 2.7 - - - +
144g TYR* 3.6 21.3 - - - +
145g LEU 3.5 13.2 - - - +
146g ALA 3.5 3.1 - - - -
147g GLN* 1.3 94.6 - - + +
149g LEU* 1.3 59.1 + - + +
151g ARG* 3.9 1.7 - - + +
152g GLU* 2.9 28.8 + - - +
133p ALA* 3.9 26.9 - - + +
136p ALA* 5.0 2.0 - - + -
137p VAL* 5.9 0.4 - - + -
161p ALA* 4.5 8.8 - - + +
165p ASN* 3.7 35.8 + - + +
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Residues in contact with LEU 149 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145g LEU 4.1 15.5 - - - +
146g ALA* 3.0 7.0 + - - +
148g PRO* 1.3 74.6 - - - +
150g LEU* 1.3 67.1 + - - +
152g GLU* 3.1 18.8 + - - +
153g VAL* 3.0 28.9 + - - +
168g LEU* 4.9 6.5 - - + -
171g ARG* 4.9 6.3 - - + +
172g CYS* 4.1 22.4 - - - +
175g VAL* 3.8 28.9 - - + -
136p ALA* 4.2 23.6 - - + +
137p VAL* 4.5 14.4 - - + -
140p ASP* 4.6 18.6 - - + +
141p LYS* 4.9 3.4 - - - +
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Residues in contact with LEU 150 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12g LEU* 4.1 23.1 - - + -
13g GLY 4.6 4.3 - - - +
14g VAL* 4.7 16.4 - - + -
136g SER* 3.9 18.8 - - - -
137g LEU 4.5 6.3 - - - +
138g ALA* 4.8 0.2 - - + -
146g ALA* 3.0 20.3 + - + +
147g GLN* 3.8 17.7 - - - +
149g LEU* 1.3 76.4 - - - +
151g ARG* 1.3 56.5 + - - +
153g VAL* 3.3 2.5 + - - +
154g LEU* 3.0 36.4 + - + +
168g LEU* 3.7 39.0 - - + +
169g VAL* 5.3 3.1 - - + +
172g CYS* 3.7 11.0 - - - -
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Residues in contact with ARG 151 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35f ILE* 2.2 50.1 + - - +
36f HIS 3.8 6.1 + - - -
37f THR* 5.6 1.2 - - - +
38f ARG* 3.7 28.2 - - - +
135g PRO* 6.2 1.8 - - + -
136g SER* 4.1 13.5 - - - +
147g GLN* 2.9 52.6 + - + +
148g PRO* 4.1 2.7 - - - +
150g LEU* 1.3 75.0 - - - +
152g GLU* 1.3 64.6 + - - +
154g LEU* 3.8 4.6 - - - +
155g GLU* 3.0 41.9 + - + +
165p ASN* 2.5 41.2 + - - +
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Residues in contact with GLU 152 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148g PRO 2.9 20.5 + - - +
149g LEU* 3.1 20.8 + - - +
151g ARG* 1.3 77.3 - - - +
153g VAL* 1.3 70.8 + - - +
155g GLU* 3.6 3.6 + - - +
156g LYS* 3.6 19.0 + - + +
171g ARG* 4.7 4.9 + - - -
137p VAL* 5.5 1.9 - - - +
141p LYS* 2.6 35.2 + - - -
157p GLU* 3.0 13.4 - - + +
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Residues in contact with VAL 153 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149g LEU 3.0 15.8 + - - +
150g LEU 3.6 7.0 - - - +
152g GLU* 1.3 85.6 - - - +
154g LEU* 1.3 62.3 - - + +
155g GLU 3.1 0.4 - - - -
156g LYS* 2.9 8.4 + - - +
157g GLN* 2.9 33.7 + - - +
160g LEU* 3.9 22.9 - - + -
168g LEU* 3.7 38.6 - - + -
171g ARG* 4.9 9.2 - - - +
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Residues in contact with LEU 154 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14g VAL* 4.1 9.9 - - + -
15g LYS 5.0 2.9 - - - +
135g PRO* 3.8 28.7 - - + +
136g SER* 3.6 32.8 - - - +
150g LEU* 3.0 19.9 + - + +
151g ARG* 3.3 4.7 + - - +
153g VAL* 1.3 79.0 - - + +
155g GLU* 1.3 59.8 + - + +
156g LYS 3.4 1.1 - - - -
157g GLN 4.0 4.5 - - - +
158g PRO* 3.4 45.8 - - - +
160g LEU* 3.8 30.7 - - + -
168g LEU* 5.4 0.9 - - + -
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Residues in contact with GLU 155 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38f ARG* 4.0 30.9 + - - -
212f LYS* 5.6 7.5 - - - +
151g ARG* 3.0 30.1 + - - +
152g GLU* 4.1 4.7 - - - +
154g LEU* 1.3 79.5 - - + +
156g LYS* 1.3 59.2 + - - +
158g PRO* 5.1 4.5 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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