Contacts of the helix formed by residues 141 - 153 (chain t) 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 ALA 141 (chain t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11t THR* 3.5 26.8 + - + +
139t GLY 3.4 0.6 - - - -
140t SER* 1.3 77.5 + - - +
142t SER* 1.3 63.8 + - - +
143t ALA 3.3 2.5 - - - -
144t MET* 2.9 22.6 + - + +
145t LEU* 3.0 14.2 + - + +
182t ALA* 4.1 16.2 - - + -
186t ASP* 3.3 24.2 - - + +
189t THR* 3.7 4.3 - - - +
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Residues in contact with SER 142 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25s TYR* 3.3 20.9 + - - -
11t THR* 5.3 0.2 - - - -
137t ALA* 2.7 34.6 + - - +
138t GLY* 3.7 10.8 - - - -
139t GLY 3.1 17.6 + - - -
140t SER 3.1 4.8 + - - -
141t ALA* 1.3 77.2 - - - +
143t ALA* 1.3 59.3 + - - +
145t LEU* 3.3 1.7 + - - +
146t GLN* 2.9 28.6 + - - +
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Residues in contact with ALA 143 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144c GLU* 4.6 16.2 - - + +
145c GLN* 3.4 24.0 - - - +
25s TYR* 2.8 42.2 - - + -
140t SER 4.8 1.4 + - - -
141t ALA 3.3 0.2 - - - -
142t SER* 1.3 80.7 - - - +
144t MET* 1.3 58.3 + - - +
147t PRO* 3.3 22.6 - - - +
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Residues in contact with MET 144 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24b MET 5.1 0.4 - - - +
25b VAL* 3.9 26.5 - - + -
144c GLU* 3.3 34.3 - - + +
145c GLN* 4.8 0.2 - - - +
147c TYR* 4.2 1.3 - - - -
148c GLY* 3.8 31.6 - - - +
140t SER 5.6 0.9 - - - +
141t ALA* 2.9 20.6 + - + +
143t ALA* 1.3 78.7 - - - +
145t LEU* 1.3 68.2 + - + +
147t PRO* 3.5 8.9 - - - +
148t LEU* 4.5 4.0 + - - +
182t ALA* 5.0 7.9 - - + -
185t ARG* 3.7 46.7 - - + +
186t ASP* 3.9 14.4 - - + +
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Residues in contact with LEU 145 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11t THR* 3.7 26.2 - - + -
13t LEU* 4.4 21.1 - - + -
137t ALA* 3.6 24.2 - - + -
141t ALA* 3.0 12.3 + - + +
144t MET* 1.3 79.0 - - + +
146t GLN* 1.3 68.2 + - - +
148t LEU* 3.2 16.1 + - + +
149t LEU* 3.3 21.2 + - + +
178t VAL* 3.6 37.5 - - + +
179t PHE* 4.4 11.0 - - + -
182t ALA* 3.7 17.0 - - + -
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Residues in contact with GLN 146 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177c ARG* 3.0 31.8 + - - +
25s TYR* 3.3 24.2 - - + +
27s ALA 5.2 0.7 - - - +
135t PHE* 3.7 14.2 + - - -
136t LYS* 3.3 29.2 + - - +
137t ALA 3.1 32.0 - - - +
142t SER 2.9 13.8 + - - +
145t LEU* 1.3 77.3 - - - +
147t PRO* 1.3 66.9 - - + +
149t LEU* 3.4 5.3 + - - +
150t ASP* 3.0 41.4 + - - +
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Residues in contact with PRO 147 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145c GLN* 3.9 22.0 - - + +
149c MET* 3.1 30.0 - - + +
173c ASN* 4.0 15.4 - - - +
177c ARG* 4.4 8.7 - - + -
25s TYR* 5.7 0.2 - - + -
143t ALA 3.3 25.8 - - - +
144t MET 3.5 7.4 - - - +
145t LEU 3.4 4.0 - - - -
146t GLN* 1.3 93.3 - - + +
148t LEU* 1.3 62.2 + - - +
150t ASP* 3.3 11.8 + - - +
151t ASN* 3.2 20.4 + - - +
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Residues in contact with LEU 148 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202b TYR* 4.0 7.9 - - + +
148c GLY 4.7 3.8 - - - +
149c MET* 3.6 17.0 - - + -
152c SER* 2.9 41.7 - - - +
153c LEU* 4.3 8.7 - - + -
144t MET 4.5 5.4 + - - +
145t LEU* 3.2 11.0 + - + +
147t PRO* 1.3 78.4 - - - +
149t LEU* 1.3 57.5 + - - +
151t ASN* 2.8 16.1 + - - +
152t GLN* 2.8 53.2 + - + +
174t LEU* 5.4 0.2 - - + -
178t VAL* 3.4 30.1 - - + -
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Residues in contact with LEU 149 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13t LEU* 3.4 39.3 - - + -
15t ILE* 4.9 11.7 - - + -
135t PHE* 3.4 36.2 - - + -
136t LYS 4.9 0.2 - - - -
137t ALA* 4.4 2.5 - - + +
145t LEU* 3.3 24.6 + - + +
146t GLN* 3.7 13.5 - - - +
148t LEU* 1.3 74.0 - - - +
150t ASP* 1.3 64.2 + - - +
152t GLN* 4.5 1.3 - - - +
153t VAL* 3.0 34.7 + - + +
154t GLY 3.4 0.2 + - - -
174t LEU* 4.6 11.0 - - + -
175t VAL* 5.9 0.4 - - + -
178t VAL* 4.3 23.6 - - + -
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Residues in contact with ASP 150 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173c ASN* 4.8 5.6 - - + +
177c ARG* 2.8 43.5 + - + +
135t PHE* 3.2 25.0 - - - -
146t GLN* 3.0 23.3 + - - +
147t PRO* 3.4 9.4 - - + +
149t LEU* 1.3 77.2 - - - +
151t ASN* 1.3 57.3 + - - +
154t GLY* 3.5 7.1 + - - -
156t LYS* 3.2 54.5 + - + +
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Residues in contact with ASN 151 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204b CYS* 5.0 2.8 - - - -
149c MET* 4.5 2.5 - - + -
153c LEU* 4.5 10.9 - - - +
169c GLN* 3.0 29.0 + - - +
173c ASN* 3.6 15.4 - - - +
147t PRO 3.2 10.9 + - - +
148t LEU* 2.8 19.5 + - + +
150t ASP* 1.3 77.2 - - - +
152t GLN* 1.3 82.3 + - - +
153t VAL 3.4 0.2 - - - -
155t PHE* 3.1 25.8 + - - -
156t LYS 3.3 15.0 + - - -
158t MET* 3.3 23.5 - - - +
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Residues in contact with GLN 152 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201b ARG 5.0 0.5 - - - +
202b TYR* 2.9 62.1 + - + +
204b CYS* 4.4 9.5 - - - -
148t LEU* 2.8 29.0 + - + +
151t ASN* 1.3 95.7 + - - +
153t VAL* 1.3 61.1 + - + +
155t PHE* 3.9 6.1 - - - -
158t MET* 4.4 6.2 - - - +
170t ARG* 3.1 47.3 + - - +
174t LEU* 4.0 21.2 - - + +
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Residues in contact with VAL 153 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15t ILE* 4.7 11.4 - - + -
16t ALA 6.2 0.4 - - - +
134t SER* 5.5 2.7 - - - +
135t PHE* 3.7 25.6 - - + -
149t LEU* 3.0 28.7 + - + +
152t GLN* 1.3 83.4 - - - +
154t GLY* 1.3 59.5 + - - +
155t PHE* 3.4 16.9 - - - -
166t LEU* 4.1 25.6 - - + -
170t ARG* 5.1 1.6 - - - +
174t LEU* 3.6 26.7 - - + -
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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
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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