Contacts of the helix formed by residues 124 - 134 (chain B) in PDB entry 3SN5
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 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B PRO* 5.6 1.8 - - - -
122B THR 3.8 2.0 + - - +
123B GLU* 1.3 73.3 - - - +
125B ILE* 1.4 60.0 + - - +
126B ASN* 3.1 25.0 + - - +
127B ASP* 2.9 39.8 + - + +
128B THR* 3.1 11.8 + - - -
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Residues in contact with ILE 125 (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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102B PHE* 3.7 34.8 - - + -
114B ILE* 3.9 13.5 - - + +
121B THR* 6.1 2.0 - - + -
123B GLU* 3.5 25.8 + - + +
124B ASN* 1.4 69.6 + - - +
126B ASN* 1.3 59.5 + - + +
128B THR* 3.0 11.3 + - - -
129B PHE* 2.9 49.3 + - + -
260B ARG* 4.8 0.4 - - - +
601B HEM 4.0 9.9 - - - +
1429B K2B 3.4 52.9 - - + -
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Residues in contact with ASN 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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266A THR* 4.5 7.4 - - - +
267A LEU* 4.3 15.2 - - - +
124B ASN* 3.1 15.7 + - - +
125B ILE* 1.3 81.9 - - + +
127B ASP* 1.4 56.3 + - - +
129B PHE* 3.4 11.7 + - - +
130B ILE* 3.0 55.6 + - - +
441B ALA 5.1 7.1 - - - +
443B ILE 5.7 0.3 - - - +
445B PRO* 5.5 4.5 - - - +
601B HEM 4.4 11.3 - - - +
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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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127A ASP* 5.5 2.6 - - - +
124B ASN* 2.9 34.2 + - + +
126B ASN* 1.4 77.6 - - - +
128B THR* 1.4 56.5 + - - +
130B ILE* 3.5 11.6 + - - +
131B LYS* 2.8 67.6 + - - +
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Residues in contact with THR 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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123B GLU* 2.8 24.6 + - - +
124B ASN 3.1 10.8 + - - -
125B ILE* 3.0 10.0 + - - -
127B ASP* 1.4 76.4 + - - +
129B PHE* 1.3 56.4 + - + +
131B LYS* 3.6 1.4 + - - +
132B THR* 2.8 34.1 + - - +
256B LEU* 4.5 5.6 - - + -
259B LEU* 4.2 26.7 - - + -
260B ARG* 3.7 32.8 - - + -
263B LEU* 3.4 13.1 - - + +
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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
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125B ILE* 2.9 40.3 + - + +
126B ASN* 3.8 5.8 - - - +
128B THR* 1.3 73.2 - - + +
130B ILE* 1.3 58.5 + - - +
132B THR* 3.3 3.7 + - - -
133B LEU* 2.9 43.7 + - + +
256B LEU* 3.7 20.9 - - + -
260B ARG* 4.6 6.1 - - - -
282B VAL* 4.0 20.2 - - + -
445B PRO* 3.7 26.5 - - + -
601B HEM 3.5 58.3 - - + -
1429B K2B 3.8 24.0 - - + -
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Residues in contact with ILE 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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259A LEU* 3.8 27.1 - - + -
262A PHE* 3.4 27.6 - - + -
263A LEU* 3.8 19.1 - - + -
266A THR* 3.8 18.2 - - + -
267A LEU* 4.8 4.9 - - + -
126B ASN* 3.0 47.6 + - - +
127B ASP* 3.8 12.1 - - - +
129B PHE* 1.3 75.6 - - + +
131B LYS* 1.3 66.0 + - + +
132B THR 3.1 1.4 + - - -
133B LEU 3.6 1.9 + - - -
134B GLN* 3.2 25.6 + - - +
445B PRO* 5.7 1.6 - - + -
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Residues in contact with LYS 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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131A LYS* 5.5 11.7 - - - -
259A LEU* 6.0 0.2 - - - -
127B ASP* 2.8 48.7 + - - +
128B THR 3.8 5.4 - - - +
130B ILE* 1.3 78.6 - - + +
132B THR* 1.3 63.2 + - + +
134B GLN* 3.9 12.7 + - - +
137B ALA* 3.8 11.1 - - - +
259B LEU* 4.3 17.2 - - + +
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Residues in contact with THR 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 THR* 2.8 21.7 + - + +
129B PHE 3.6 2.1 + - - -
130B ILE 3.2 0.6 - - - -
131B LYS* 1.3 80.2 - - + +
133B LEU* 1.3 66.3 + - - +
134B GLN 3.6 2.5 - - - -
137B ALA* 3.3 25.7 - - - +
141B LEU* 4.5 5.0 - - - +
255B GLU* 3.6 28.6 - - + +
256B LEU* 3.3 39.6 + - - +
259B LEU* 3.8 19.1 - - + -
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Residues in contact with LEU 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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262A PHE* 4.2 6.5 - - + -
129B PHE* 2.9 32.9 + - + +
130B ILE 3.6 0.6 + - - -
132B THR* 1.3 81.3 - - - +
134B GLN* 1.4 59.5 + - - +
138B LEU* 3.7 24.3 - - - +
141B LEU* 3.6 27.1 - - + -
256B LEU* 4.3 11.2 - - + -
445B PRO* 3.5 48.6 - - + +
446B GLY* 3.9 9.4 - - - +
448B LEU* 4.6 3.3 - - - +
449B PHE* 4.8 5.8 + - + -
601B HEM 4.1 28.5 - - + -
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Residues in contact with GLN 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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258A SER* 3.6 2.5 + - - +
259A LEU* 3.5 40.5 + - + +
262A PHE* 3.5 41.3 - - + -
2134A UNX 3.6 12.5 - - - -
130B ILE 3.2 26.8 + - - +
131B LYS* 3.9 12.3 + - - +
133B LEU* 1.4 77.4 - - - +
135B GLY* 1.3 82.0 + - - +
137B ALA* 3.3 9.7 + - - +
138B LEU* 3.0 20.4 + - - -
448B LEU* 4.7 5.2 - - + -
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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