Contacts of the helix formed by residues 129 - 145 (chain B) in PDB entry 5FQU
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B GLY* 1.3 67.6 + - - +
131B VAL* 3.2 6.0 - - - +
132B ILE* 3.5 22.0 + - + +
133B GLN* 3.2 53.0 + - + +
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 1.3 77.6 - - - +
131B VAL* 1.3 57.3 + - - +
134B GLY 3.2 15.8 + - - -
193B ALA 5.9 2.0 - - - -
194B VAL 4.1 16.3 - - - +
195B PHE* 3.7 2.6 - - - -
196B ALA* 2.9 30.1 + - - -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 3.2 3.0 - - - +
130B GLY* 1.3 76.6 - - - +
132B ILE* 1.3 61.2 + - + +
134B GLY* 3.3 1.6 + - - +
135B GLN* 3.0 46.9 + - + +
196B ALA* 3.9 20.2 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.5 23.4 + - + +
131B VAL* 1.3 76.5 - - + +
133B GLN* 1.3 65.8 + - + +
135B GLN* 3.4 15.1 + - - +
136B ASN* 2.9 42.8 + - - +
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLN 5.9 1.4 + - - -
129B LEU* 3.2 40.6 + - + +
130B GLY* 5.2 0.2 - - - -
132B ILE* 1.3 77.3 - - + +
134B GLY* 1.3 60.8 + - - +
136B ASN* 3.8 9.4 - - - +
137B LEU* 2.9 32.6 + - - +
194B VAL* 2.9 39.5 - - - +
195B PHE* 3.5 14.8 - - + -
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY 3.2 15.4 + - - -
131B VAL* 3.3 5.8 + - - -
132B ILE 3.3 0.4 - - - -
133B GLN* 1.3 77.1 - - - +
135B GLN* 1.3 60.5 + - - +
138B ALA* 3.2 12.1 + - - +
186B ARG* 2.8 50.2 + - - -
195B PHE* 3.9 5.6 - - - -
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B VAL* 3.0 32.8 + - + +
132B ILE* 3.8 17.4 - - - +
134B GLY* 1.3 73.6 - - - +
136B ASN* 1.3 65.7 + - - +
138B ALA* 2.9 18.8 + - - +
139B MSE 3.0 32.8 + - + +
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Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 2.9 35.9 + - - +
133B GLN* 3.8 9.8 - - - +
135B GLN* 1.3 75.2 - - - +
137B LEU* 1.3 60.8 + - - +
139B MSE 3.3 22.0 + - - +
140B VAL* 3.1 29.6 + - + +
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 5.6 2.2 - - + -
133B GLN 2.9 17.4 + - - +
134B GLY 4.0 3.6 - - - +
136B ASN* 1.3 74.4 - - - +
138B ALA* 1.3 58.9 + - - +
140B VAL* 3.4 8.1 + - + +
141B LEU* 3.0 55.2 + - + +
186B ARG* 4.0 16.4 - - - +
189B MSE 3.7 36.8 - - + -
195B PHE* 3.9 35.0 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY 3.2 12.0 + - - +
135B GLN* 2.9 13.2 + - - +
137B LEU* 1.3 80.0 - - - +
139B MSE 1.3 59.4 + - + +
141B LEU* 4.0 5.9 - - - +
142B GLU* 3.2 37.4 + - - +
182B PRO* 5.2 1.0 - - - +
186B ARG* 3.9 19.3 - - + +
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Residues in contact with MSE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLN* 3.0 35.9 + - + +
136B ASN* 3.4 29.4 - - - +
137B LEU 3.3 0.2 - - - -
138B ALA* 1.3 77.7 - - + +
140B VAL* 1.3 65.2 + - + +
142B GLU* 3.5 12.1 + - - +
143B SER* 2.9 27.4 + - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B MSE 5.1 25.1 - - + -
136B ASN* 3.1 19.9 + - + +
137B LEU* 3.8 9.6 - - + +
139B MSE 1.3 78.1 - - + +
141B LEU* 1.3 65.6 + - + +
143B SER* 3.0 8.1 + - - -
144B LEU* 3.0 43.5 + - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 4.5 19.1 - - + -
68B LEU* 5.4 4.9 - - + -
137B LEU* 3.0 38.9 + - + +
138B ALA* 4.0 4.3 - - - +
140B VAL* 1.3 79.5 - - + +
142B GLU* 1.3 56.9 + - - +
144B LEU* 4.0 12.5 - - + +
145B LEU* 3.1 41.9 + - + +
182B PRO* 3.9 14.6 - - + +
185B ILE* 3.7 22.7 - - + -
186B ARG* 3.7 40.2 - - + +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ALA* 3.2 23.4 + - - +
139B MSE 4.0 13.7 - - - +
140B VAL 3.2 0.8 - - - -
141B LEU* 1.3 75.3 - - - +
143B SER* 1.3 58.6 + - - +
145B LEU 3.6 0.9 - - - -
146B VAL* 3.0 30.3 + - - +
182B PRO* 3.7 25.2 - - + +
183B GLN* 5.8 1.4 + - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MSE 2.9 15.0 + - - -
140B VAL* 3.0 11.4 + - - -
142B GLU* 1.3 76.9 - - - +
144B LEU* 1.3 68.1 + - - +
145B LEU 3.3 0.5 + - - -
146B VAL* 3.5 21.4 + - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.8 32.1 - - + -
73B TYR* 2.9 40.4 + - + +
81B ILE* 3.7 36.6 - - + -
140B VAL* 3.0 36.4 + - + +
141B LEU* 4.1 10.1 - - + +
143B SER* 1.3 83.4 - - - +
145B LEU* 1.3 60.9 + - - +
146B VAL* 3.6 1.4 + - - +
147B HIS* 3.8 6.2 + - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.9 23.6 - - + -
71B SER* 3.4 35.0 - - - +
141B LEU* 3.1 26.1 + - + +
142B GLU 3.6 2.2 - - - -
143B SER 3.1 0.4 - - - -
144B LEU* 1.3 79.7 - - - +
146B VAL* 1.3 53.5 + - - +
147B HIS* 3.0 7.0 - - + -
148B THR* 2.7 44.4 + - - +
149B SER 4.1 0.2 + - - -
181B LEU* 4.1 20.0 - - + -
182B PRO* 4.0 28.6 - - + +
185B ILE* 4.3 12.1 - - + -
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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
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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