Contacts of the helix formed by residues 125 - 140 (chain B) in PDB entry 1F5Q
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 THR 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 3.5 9.9 - - - -
123B ALA 3.6 11.1 + - - +
124B THR* 1.3 80.3 - - - +
126B ALA* 1.3 65.2 + - - +
127B ASP* 3.6 9.8 + - - +
128B LYS* 3.0 37.6 + - + +
129B LEU* 3.0 14.9 + - - +
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Residues in contact with ALA 126 (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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41A THR 5.9 1.3 - - - +
113B ALA* 3.9 18.6 - - + -
114B THR* 3.7 39.9 - - + +
117B ALA* 3.6 5.2 - - - +
125B THR* 1.3 73.0 - - - +
127B ASP* 1.3 68.1 + - - +
129B LEU* 3.1 4.4 + - - +
130B LEU* 2.9 32.5 + - + +
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Residues in contact with ASP 127 (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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125B THR* 3.1 10.6 + - - +
126B ALA* 1.3 82.2 - - - +
128B LYS* 1.3 60.9 + - + +
130B LEU* 3.6 9.7 + - - +
131B THR* 3.2 25.5 + - - -
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Residues in contact with LYS 128 (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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93B SER* 6.1 0.9 - - - +
123B ALA* 3.8 28.5 - - + +
124B THR* 4.8 4.7 - - + -
125B THR* 3.0 22.4 + - - +
127B ASP* 1.3 76.6 - - + +
129B LEU* 1.3 68.2 + - + +
131B THR* 3.3 6.8 + - - +
132B LEU* 3.1 23.4 + - - +
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Residues in contact with LEU 129 (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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93B SER* 3.7 42.0 - - - +
96B ALA* 4.1 12.6 - - + -
97B VAL* 3.5 11.0 - - + +
100B HIS* 6.2 3.8 - - + +
113B ALA* 3.7 16.4 - - + +
116B LEU* 4.1 13.2 - - + -
117B ALA* 3.6 37.5 - - + +
124B THR* 4.0 9.6 - - + -
125B THR 3.0 12.1 + - - +
126B ALA* 3.6 6.1 - - - +
128B LYS* 1.3 77.9 - - + +
130B LEU* 1.3 58.4 + - - +
132B LEU* 3.3 6.3 + - + +
133B GLU* 2.9 27.4 + - - +
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Residues in contact with LEU 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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40A GLU 4.8 1.6 - - - +
41A THR 3.3 25.8 - - - +
42A GLU* 3.5 21.1 - - - +
43A GLY* 3.9 14.4 - - - +
100B HIS* 3.8 15.0 - - + +
113B ALA* 4.4 10.1 - - + -
126B ALA* 2.9 22.2 + - + +
127B ASP* 4.0 9.4 - - - +
129B LEU* 1.3 74.1 - - + +
131B THR* 1.3 65.3 + - - +
132B LEU 3.2 0.2 - - - -
133B GLU* 3.3 19.9 + - - +
134B VAL* 3.3 25.6 + - - +
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Residues in contact with THR 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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127B ASP 3.2 18.0 + - - -
128B LYS* 3.3 6.9 + - - +
130B LEU* 1.3 76.3 - - - +
132B LEU* 1.3 59.9 + - - +
134B VAL* 3.6 7.5 + - - +
135B LYS* 3.1 40.7 + - + +
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Residues in contact with LEU 132 (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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90B ASN* 4.8 7.6 - - + +
93B SER* 4.0 29.2 - - - +
94B THR* 4.0 13.5 - - - +
97B VAL* 3.6 21.5 - - + -
128B LYS 3.1 13.4 + - - +
129B LEU* 3.5 9.6 - - + +
131B THR* 1.3 77.9 - - + +
133B GLU* 1.3 54.8 + - - +
134B VAL 3.3 0.2 - - - -
135B LYS* 3.6 21.0 + - + +
136B SER* 2.7 44.2 + - - +
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Residues in contact with GLU 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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42A GLU 3.8 0.3 - - - +
44A VAL* 4.2 10.5 + - + +
97B VAL* 3.7 13.2 - - + -
100B HIS* 2.4 35.6 + - - +
101B ILE* 3.6 28.6 + - + +
104B LYS* 2.9 29.1 + - - -
129B LEU 2.9 15.9 + - - +
130B LEU* 3.6 19.8 - - - +
131B THR 3.3 0.4 - - - -
132B LEU* 1.3 75.8 - - - +
134B VAL* 1.3 60.9 + - + +
136B SER* 3.7 0.3 - - - -
137B LEU* 2.9 38.0 + - + +
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Residues in contact with VAL 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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37A LEU* 4.5 17.3 - - + +
44A VAL* 5.0 7.0 - - + -
71A HIS* 3.3 37.2 - - + +
130B LEU 3.3 12.4 + - - +
131B THR* 3.9 9.2 - - - +
132B LEU 3.3 0.4 - - - -
133B GLU* 1.3 76.9 - - + +
135B LYS* 1.3 64.1 + - + +
137B LEU* 3.3 2.5 + - - +
138B ASP* 2.9 30.1 + - - +
142B TRP* 3.9 19.9 - - + -
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Residues in contact with LYS 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 THR* 3.1 36.1 - - + +
132B LEU* 3.8 20.6 - - + +
133B GLU 3.3 0.2 - - - -
134B VAL* 1.3 79.5 - - + +
136B SER* 1.3 61.4 + - - +
138B ASP* 3.5 11.0 + - - +
139B THR* 3.1 23.2 + - - -
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Residues in contact with SER 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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80B LEU* 3.9 28.6 - - - +
94B THR* 5.7 1.7 - - - +
97B VAL* 3.7 20.7 - - - +
101B ILE* 4.2 4.3 - - - -
132B LEU* 2.7 32.1 + - - +
133B GLU 3.7 4.3 - - - -
134B VAL 3.2 0.2 - - - -
135B LYS* 1.3 75.0 - - - +
137B LEU* 1.3 60.5 + - - +
139B THR* 2.9 20.7 + - - -
140B LEU* 3.0 17.0 + - - +
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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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44A VAL* 3.9 14.6 - - + -
49A ILE* 4.3 12.3 - - + -
101B ILE* 3.8 31.4 - - + -
104B LYS* 5.7 1.3 - - + +
133B GLU* 2.9 33.1 + - + +
134B VAL 3.8 2.0 - - - +
136B SER* 1.3 76.5 - - - +
138B ASP* 1.3 56.9 - - - +
140B LEU* 3.2 8.8 + - + +
141B SER 2.9 8.3 + - - -
142B TRP* 2.7 77.9 + - + -
144B ALA* 4.2 14.4 - - + -
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Residues in contact with ASP 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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71A HIS* 2.6 45.0 + - - +
134B VAL* 2.9 18.3 + - - +
135B LYS* 3.5 10.4 - - - +
137B LEU* 1.3 76.7 - - - +
139B THR* 1.3 63.5 + - - +
141B SER* 3.3 12.0 + - - -
142B TRP* 3.1 16.1 + - - +
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Residues in contact with THR 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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79B GLU* 4.9 5.3 - - - +
80B LEU* 3.9 20.8 - - + +
83B SER* 4.1 18.2 - - - +
84B THR* 3.8 28.9 - - + +
135B LYS 3.1 12.5 + - - -
136B SER* 2.9 13.2 + - - -
138B ASP* 1.3 81.1 - - - +
140B LEU* 1.3 58.6 + - + +
141B SER* 3.2 7.8 + - - -
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Residues in contact with LEU 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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76B LEU* 3.9 25.8 - - + -
79B GLU* 3.7 29.2 - - + +
80B LEU* 4.3 20.6 - - + -
101B ILE* 4.7 9.4 - - + -
136B SER 3.0 19.5 + - - +
137B LEU* 3.2 19.2 + - + +
139B THR* 1.3 76.7 - - + +
141B SER* 1.3 70.5 + - - +
142B TRP 3.0 2.4 + - - +
143B VAL* 3.0 28.9 + - - +
144B ALA* 5.2 1.3 - - - -
146B ARG* 3.5 22.5 + - - +
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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