Contacts of the helix formed by residues 139 - 150 (chain L) 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 SER 139 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138L LEU* 1.3 68.0 - - - +
140L GLU* 1.3 69.7 + - - -
141L GLN 3.7 0.9 - - - -
142L ILE* 4.1 19.0 - - - +
143L ARG* 3.3 35.6 + - - +
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Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L LEU* 1.7 41.6 + - + +
139L SER* 1.3 79.9 + - - +
141L GLN* 1.3 63.7 + - + +
143L ARG* 4.0 23.7 + - - +
144L GLU* 2.7 43.8 + - - +
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Residues in contact with GLN 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138L LEU* 2.6 45.4 - - + +
140L GLU* 1.3 80.1 - - + +
142L ILE* 1.3 59.8 + - - +
144L GLU* 3.7 11.7 - - - +
145L LEU* 2.5 36.2 + - + +
183L LEU* 4.8 10.8 - - + -
299L ILE* 3.2 29.8 - - + -
300L HIS 2.4 31.8 + - - +
301L ILE* 3.2 23.0 - - + +
302L ASP 4.3 1.2 - - - +
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Residues in contact with ILE 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L TYR* 4.1 33.7 - - + +
135L ILE* 4.8 16.6 - - + +
136L GLY* 3.5 32.3 - - - +
138L LEU* 4.3 10.3 - - + +
139L SER* 4.1 25.4 - - - +
141L GLN* 1.3 81.6 + - - +
143L ARG* 1.3 59.3 + - + +
145L LEU* 4.1 3.0 - - - +
146L ARG* 3.1 31.5 + - - +
183L LEU* 5.4 13.6 - - + +
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Residues in contact with ARG 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K ARG* 3.4 41.4 - - - +
401K LYS* 5.0 6.9 - - - +
139L SER* 3.3 26.8 + - - +
140L GLU* 4.0 30.8 + - - -
142L ILE* 1.3 78.3 - - + +
144L GLU* 1.3 67.3 + - - +
146L ARG* 3.6 7.8 - - - +
147L GLU* 2.0 72.8 + - - +
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Residues in contact with GLU 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K ARG* 4.2 8.6 + - - +
140L GLU* 2.7 34.8 + - - +
141L GLN* 3.0 10.1 + - - +
143L ARG* 1.3 86.6 + - - +
145L LEU* 1.3 63.1 + - - +
147L GLU* 2.9 14.1 - - - +
148L VAL* 3.4 17.9 + - - +
297L ARG* 3.0 47.5 + - - +
298L LYS 4.8 2.4 - - - +
299L ILE* 4.6 14.9 - - + +
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Residues in contact with LEU 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L GLN* 2.5 23.0 + - + +
142L ILE* 4.1 2.7 - - - +
144L GLU* 1.3 71.8 - - - +
146L ARG* 1.3 66.8 + - + +
148L VAL* 2.9 7.2 + - - -
149L ILE* 2.4 64.2 + - + +
170L CYS* 3.4 15.5 - - + -
172L LEU* 5.2 5.4 - - + -
183L LEU* 4.0 16.8 - - + -
187L VAL* 3.9 28.7 - - + -
276L ILE* 5.0 12.1 - - + -
299L ILE* 2.8 34.3 - - + +
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Residues in contact with ARG 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L TYR* 2.7 53.0 + - - +
142L ILE* 3.1 29.1 + - - +
143L ARG* 3.6 9.2 - - - +
145L LEU* 1.3 79.6 - - + +
147L GLU* 1.3 60.9 + - + +
149L ILE* 4.7 1.8 - - - -
150L GLU* 2.2 74.7 + - + +
151L LEU* 3.3 5.3 + - + -
190L GLN* 2.3 39.7 + - - +
191L LEU* 5.8 0.2 - - - +
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Residues in contact with GLU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K MET* 5.5 7.4 - - + +
388K ARG* 2.6 54.2 + - + +
143L ARG* 2.0 66.6 + - - +
144L GLU* 2.9 6.6 - - - +
146L ARG* 1.3 77.4 - - + +
148L VAL* 1.3 66.9 + - - +
151L LEU* 3.5 28.8 - - + +
152L PRO* 3.1 15.6 - - - +
159L PHE* 4.4 8.8 - - - -
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Residues in contact with VAL 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K MET* 4.6 11.4 - - + -
144L GLU 3.4 14.4 + - - +
145L LEU* 2.9 24.2 + - - +
147L GLU* 1.3 77.4 - - - +
149L ILE* 1.3 54.4 - - + +
152L PRO* 2.2 32.4 - - - +
167L PRO* 2.4 59.4 - - + +
170L CYS* 3.1 33.4 - - - -
296L ASP* 4.0 14.1 - - - +
297L ARG* 4.1 14.8 - - - +
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Residues in contact with ILE 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145L LEU* 2.4 66.3 + - + +
146L ARG* 4.1 1.3 - - - +
148L VAL* 1.3 84.5 - - + +
150L GLU* 1.3 55.3 + - + +
152L PRO* 2.9 12.2 - - - +
153L LEU* 2.6 28.8 - - - +
167L PRO* 5.4 1.1 - - + -
170L CYS* 4.5 6.1 - - + -
187L VAL* 5.2 4.3 - - + -
191L LEU* 4.1 20.6 - - + -
229L ILE* 4.1 21.1 - - + -
274L LYS* 4.6 14.3 - - + +
276L ILE* 5.0 11.7 - - + -
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Residues in contact with GLU 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L ARG* 2.2 57.9 + - + +
149L ILE* 1.3 76.6 - - - +
151L LEU* 1.3 67.2 + - + +
153L LEU* 1.9 52.2 - - + +
154L THR* 4.9 3.9 + - + +
190L GLN* 4.0 8.5 + - - +
191L LEU* 3.6 31.6 - - + +
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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