Contacts of the helix formed by residues 126 - 136 (chain B) in PDB entry 3FD4
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 ASN 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PRO* 6.4 0.4 - - - +
94B TYR* 5.1 8.2 + - - -
124B THR* 3.3 4.1 + - - +
125B TRP* 1.3 93.1 - - + +
127B GLY* 1.3 62.8 + - - +
128B CYS 3.1 3.5 + - - -
129B PHE* 3.2 38.3 + - - +
130B GLN* 4.4 0.9 + - - +
191B HIS* 5.5 3.8 - - + +
208B CYS 5.0 0.2 + - - -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 4.4 11.0 + - - -
124B THR* 3.2 21.0 + - - -
126B ASN* 1.3 75.7 - - - +
128B CYS* 1.3 56.5 + - - +
129B PHE 3.2 0.2 - - - -
130B GLN* 3.3 8.1 + - - +
131B ALA* 2.9 30.3 + - - +
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Residues in contact with CYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS* 4.2 0.4 - - - -
124B THR 3.3 14.7 + - - -
125B TRP 3.3 10.8 - - - +
126B ASN 3.1 0.8 - - - -
127B GLY* 1.3 74.0 - - - +
129B PHE* 1.3 59.9 + - - +
131B ALA* 4.0 1.8 - - - -
132B CYS* 2.9 33.8 + - - +
141B PHE* 3.3 22.6 - - + +
163B TRP* 3.8 22.7 - - - -
214B CYS* 2.0 52.9 - - + -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.4 50.2 - + + -
125B TRP* 3.8 28.7 - + - -
126B ASN* 3.2 33.3 + - - +
128B CYS* 1.3 79.2 - - - +
130B GLN* 1.3 57.1 + - - +
132B CYS* 4.2 1.6 - - - +
133B ALA* 3.1 27.4 + - - +
140B TYR* 5.4 1.0 - - - +
141B PHE* 3.8 33.0 + + + +
165B GLY* 5.3 0.7 - - - -
167B TYR* 4.0 25.1 - + - -
177B LEU* 3.6 28.7 - - + -
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.7 20.5 + - + +
126B ASN 4.4 0.6 + - - +
127B GLY* 3.3 9.0 + - - +
129B PHE* 1.3 77.0 - - - +
131B ALA* 1.3 57.5 + - - +
133B ALA* 3.0 9.4 + - + +
134B GLU* 2.8 63.0 + - + +
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Residues in contact with ALA 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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119B THR* 5.2 4.3 - - + -
123B HIS* 3.5 41.5 - - + +
127B GLY 2.9 18.1 + - - +
128B CYS* 4.0 4.9 - - - -
130B GLN* 1.3 78.1 - - - +
132B CYS* 1.4 57.6 + - - +
134B GLU* 3.3 7.7 + - - +
135B LEU* 3.1 29.7 + - - +
214B CYS* 4.5 2.5 - - - -
216B CYS* 5.1 0.4 - - - -
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Residues in contact with CYS 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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128B CYS 2.9 21.0 + - - +
129B PHE 4.2 0.4 - - - +
131B ALA* 1.4 75.2 - - - +
133B ALA* 1.3 62.7 + - - +
135B LEU* 3.2 11.3 + - - +
139B THR* 3.5 22.7 - - - +
140B TYR 3.4 21.8 - - - -
141B PHE* 3.6 12.1 - - - +
214B CYS* 3.9 11.9 - - - -
215B LEU 3.8 3.6 - - - -
216B CYS* 2.1 54.7 - - + -
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Residues in contact with ALA 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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94B TYR* 5.2 7.9 - - + -
129B PHE 3.1 16.6 + - - +
130B GLN* 3.0 13.3 + - - +
132B CYS* 1.3 76.6 - - - +
134B GLU* 1.3 62.0 + - + +
136B TYR 3.6 11.6 - - - +
137B PRO* 5.3 1.0 - - - +
138B CYS 5.6 0.5 + - - -
139B THR 3.4 14.9 + - - +
140B TYR* 4.6 1.3 - - - +
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Residues in contact with GLU 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 GLN* 2.8 50.0 + - + +
131B ALA* 3.7 5.7 - - - +
133B ALA* 1.3 75.3 - - + +
135B LEU* 1.3 65.6 + - - +
136B TYR* 3.4 2.6 - - - -
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Residues in contact with LEU 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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117B TYR* 3.7 31.6 - - + -
119B THR* 4.1 30.7 - - + -
120B LYS 5.7 1.3 - - - +
121B LYS* 4.6 17.9 - - + +
131B ALA 3.1 14.6 + - - +
132B CYS* 3.2 11.2 + - - +
134B GLU* 1.3 79.5 - - - +
136B TYR* 1.3 98.9 + - + +
139B THR* 4.9 1.3 - - + -
216B CYS* 4.3 6.7 - - + -
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Residues in contact with TYR 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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101B TYR* 3.8 16.8 - + + -
103B ASN* 3.3 27.1 - - + -
106B GLU* 3.2 24.1 + - + +
117B TYR* 3.4 44.2 - + - +
132B CYS 4.2 0.8 + - - -
133B ALA 3.6 13.6 - - - +
134B GLU 4.6 1.1 - - - -
135B LEU* 1.3 109.6 - - + +
137B PRO* 1.3 78.4 - - + +
138B CYS 3.6 0.9 + - - -
139B THR* 3.3 21.3 + - - +
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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