Contacts of the helix formed by residues 119 - 128 (chain B) in PDB entry 3I5G
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 SER 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ASN 5.4 0.2 + - - -
118B PHE* 1.3 73.3 - - - +
120B LYS* 1.3 55.7 + - - +
121B GLU* 2.7 17.9 - - - -
122B GLU* 3.1 35.9 + - - +
123B ILE* 2.7 35.5 + - - +
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Residues in contact with LYS 120 (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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112B GLU* 3.5 24.2 - - + +
118B PHE 3.9 1.0 + - - +
119B SER* 1.3 72.2 - - - +
121B GLU* 1.3 62.8 + - + +
123B ILE* 3.6 12.7 - - + +
124B LYS* 3.8 16.6 + - - +
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Residues in contact with GLU 121 (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 SER* 4.2 12.5 - - - -
120B LYS* 1.3 84.9 - - + +
122B GLU* 1.3 59.6 + - + +
123B ILE 3.1 1.3 - - - -
124B LYS* 3.4 6.4 + - - +
125B ASN* 2.7 35.4 + - - +
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Residues in contact with GLU 122 (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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818A ARG* 3.4 45.7 + - - +
821A LEU* 4.2 11.0 - - + +
117B ASN 4.3 0.2 - - - +
118B PHE* 3.7 12.3 - - + -
119B SER* 2.9 38.1 + - - +
121B GLU* 1.3 74.9 - - + +
123B ILE* 1.3 66.2 + - - +
125B ASN* 3.3 15.5 + - - +
126B VAL* 3.0 29.1 + - - +
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Residues in contact with ILE 123 (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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108B LYS* 4.9 10.8 - - + -
111B LEU* 5.8 1.3 - - + -
112B GLU* 3.0 54.1 - - + +
118B PHE* 4.0 17.3 - - + -
119B SER 2.7 26.9 + - - +
120B LYS* 3.6 14.8 - - - +
122B GLU* 1.3 78.6 - - - +
124B LYS* 1.3 58.0 + - - +
126B VAL* 3.1 10.8 + - - +
127B TRP* 2.9 57.8 + - + +
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Residues in contact with LYS 124 (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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120B LYS 3.8 10.5 + - - +
121B GLU* 3.4 8.8 + - - +
122B GLU 3.3 0.2 - - - -
123B ILE* 1.3 75.1 - - - +
125B ASN* 1.3 67.5 + - - +
126B VAL 2.8 5.2 - - - -
127B TRP* 2.6 30.5 + - + +
128B LYS* 2.9 49.9 + - - +
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Residues in contact with ASN 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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820A TRP* 4.3 1.4 - - - -
821A LEU* 3.7 26.9 - - + +
824A ARG* 3.6 34.1 + - - +
121B GLU* 2.7 24.9 + - - +
122B GLU* 3.3 19.7 - - - +
123B ILE 3.4 0.4 - - - -
124B LYS* 1.3 82.2 - - - +
126B VAL* 1.3 60.0 + - - +
128B LYS* 4.1 17.2 + - - +
129B ASP* 3.8 7.6 + - - +
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Residues in contact with VAL 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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817A VAL* 3.6 33.4 - - + -
820A TRP* 4.8 2.2 - - + -
821A LEU* 4.2 11.0 - - + -
107B LEU* 5.6 3.6 - - + -
111B LEU* 5.0 12.8 - - + -
118B PHE* 4.0 11.9 - - + -
122B GLU 3.0 15.9 - - - +
123B ILE* 3.2 11.2 - - - +
124B LYS 2.7 1.0 + - - -
125B ASN* 1.3 79.7 - - - +
127B TRP* 1.3 64.4 + - + -
129B ASP* 2.7 22.7 - - - +
130B ALA* 3.1 15.3 - - + +
137B PHE* 5.5 8.3 - - + -
142B MET* 6.0 6.1 - - + -
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Residues in contact with TRP 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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104B GLU* 3.2 42.0 - - + -
107B LEU* 4.8 13.5 - - + -
108B LYS* 4.0 33.2 - - + +
123B ILE* 2.9 49.5 + - + +
124B LYS* 2.6 24.6 + - + +
126B VAL* 1.3 75.3 - - + +
128B LYS* 1.3 64.6 + - - +
129B ASP 3.1 1.6 + - - -
130B ALA* 3.7 17.9 + - + +
132B LEU* 3.5 42.6 - - + +
137B PHE* 4.8 4.7 - + - -
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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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824A ARG* 5.6 7.6 - - - +
124B LYS* 2.9 52.2 + - + +
125B ASN* 4.1 14.7 + - - +
126B VAL 3.4 0.2 - - - -
127B TRP* 1.3 76.8 - - - +
129B ASP* 1.3 60.6 + - + +
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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