Contacts of the helix formed by residues 125 - 135 (chain B) in PDB entry 3I8C
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 ALA 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A GLU* 6.0 2.0 - - + -
910A MET* 4.2 23.3 - - + -
926A LEU* 5.8 3.8 - - + -
124B ASN* 1.3 78.2 - - - +
126B SER* 1.3 47.6 + - - +
128B MET* 2.4 34.1 - - + +
129B LEU* 2.3 44.3 + - + +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A TYR* 5.2 0.3 - - - -
814A LEU* 5.8 4.5 - - - -
836A VAL* 4.4 13.8 - - - +
843A PRO* 5.5 4.9 - - - -
871A TYR* 5.1 9.2 + - - -
124B ASN* 2.5 30.4 + - - +
125B ALA* 1.3 76.1 - - - +
127B SER* 1.3 75.0 + - - -
128B MET 2.7 0.7 - - - -
129B LEU* 3.8 11.8 - - - +
130B ARG* 2.8 52.2 + - - +
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN* 4.1 18.1 - - - +
126B SER* 1.3 85.1 + - - +
128B MET* 1.3 59.7 + - - +
130B ARG* 3.3 7.4 + - - +
131B LYS* 2.3 71.7 + - - +
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN 5.5 0.2 - - - +
125B ALA* 2.4 39.9 - - + +
126B SER 2.7 0.2 - - - -
127B SER* 1.3 82.1 - - - +
129B LEU* 1.3 65.7 + - + -
131B LYS* 4.7 10.8 - - + -
132B SER* 3.0 29.8 + - - +
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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
----------------------------------------------------------
871A TYR* 3.6 35.4 - - + -
910A MET* 4.1 10.8 - - + -
912A LEU* 4.1 24.9 - - + -
913A TYR* 5.2 2.7 - - - +
926A LEU* 5.4 7.4 - - + -
125B ALA* 2.3 39.5 + - + +
126B SER* 3.2 8.6 + - - +
128B MET* 1.3 68.9 - - + +
130B ARG* 1.3 58.0 + - + +
131B LYS 2.8 2.2 - - - -
132B SER* 3.2 6.9 + - - +
133B GLN* 2.5 57.3 + - - +
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Residues in contact with ARG 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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722A ARG* 2.3 45.7 - - - +
787A GLU* 3.4 14.1 + - - +
789A HIS* 4.5 0.2 - - - -
812A TYR* 2.5 59.4 - - - +
814A LEU* 3.1 33.3 - - - +
126B SER* 2.8 36.9 + - - +
127B SER* 3.9 6.9 - - - +
129B LEU* 1.3 77.5 - - + +
131B LYS* 1.3 61.3 + - + +
133B GLN* 3.0 14.9 + - - +
134B LEU* 2.8 36.5 + - + +
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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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127B SER* 2.3 52.5 + - - +
128B MET* 3.9 11.7 - - + +
129B LEU 2.7 3.2 + - - -
130B ARG* 1.3 79.6 - - - +
132B SER* 1.3 64.9 + - - +
133B GLN 2.4 6.6 + - - -
134B LEU* 3.1 4.9 + - + +
135B GLY 2.7 28.4 + - - +
136B PHE 4.7 9.0 - - - +
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Residues in contact with SER 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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970A ASN* 5.5 5.6 - - - -
1003A PHE* 3.7 29.7 - - - -
1033A VAL* 4.7 0.5 - - - +
128B MET* 3.0 19.3 + - - +
129B LEU* 3.2 14.6 + - - +
131B LYS* 1.3 77.6 - - - +
133B GLN* 1.3 71.3 + - - +
135B GLY* 3.4 9.8 + - - -
136B PHE* 6.0 0.4 - - - +
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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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360A VAL* 4.9 15.6 - - + +
722A ARG* 5.8 4.0 - - - -
723A LYS* 5.4 7.7 - - - +
913A TYR* 5.2 12.5 + - - -
1003A PHE* 4.9 2.9 - - + -
1005A ASN* 4.1 25.2 + - - +
1033A VAL* 3.2 18.5 - - - +
129B LEU* 2.5 39.3 + - + +
130B ARG* 3.2 16.5 - - - +
131B LYS 2.4 6.5 - - - -
132B SER* 1.3 89.2 - - - +
134B LEU* 1.3 62.1 + - + +
135B GLY 2.9 5.5 + - - -
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Residues in contact with LEU 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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327A ARG* 2.9 22.5 + - - -
328A LEU* 4.2 12.1 - - + +
358A PRO* 4.3 13.9 - - + +
360A VAL* 3.8 27.1 - - + -
380A GLY 4.4 2.5 - - - +
381A ALA* 4.0 27.8 - - + -
382A PHE* 4.4 18.2 - - + -
720A SER* 6.4 0.7 - - - -
1033A VAL* 4.2 7.2 - - - +
130B ARG* 2.8 28.0 + - + +
131B LYS* 3.1 4.4 + - + +
133B GLN* 1.3 74.5 - - + +
135B GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 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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327A ARG* 4.3 5.1 + - - -
1033A VAL* 4.1 15.7 - - - -
131B LYS* 2.7 14.5 + - - +
132B SER* 3.4 7.2 + - - -
133B GLN 2.9 8.6 + - - -
134B LEU* 1.3 82.1 - - - +
136B PHE* 1.3 76.9 + - - +
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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