Contacts of the helix formed by residues 120 - 135 (chain B) in PDB entry 1I4L
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 LYS 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B THR* 3.3 21.0 + - + +
119B THR* 1.3 92.5 + - - +
121B THR* 1.3 62.0 + - - +
122B MET 3.2 1.6 - - - -
123B GLU* 2.8 4.9 + - - +
124B ASP* 2.7 35.7 + - - +
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Residues in contact with THR 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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116B THR* 3.3 20.4 + - - +
117B LEU* 4.2 11.0 - - + -
120B LYS* 1.3 79.7 - - - +
122B MET* 1.3 62.8 + - - +
124B ASP* 3.5 8.9 + - - +
125B THR* 3.4 19.8 + - - -
190B LEU* 3.2 26.5 - - + -
193B ASN* 4.0 21.0 + - - +
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Residues in contact with MET 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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37B LEU* 3.2 45.3 - - + +
40B THR* 4.4 9.9 - - + -
41B LYS* 3.3 35.7 - - + +
44B TYR* 5.1 5.2 - - - -
117B LEU* 2.8 37.5 + - + +
118B VAL* 3.7 22.9 - - + +
120B LYS 3.2 0.6 - - - -
121B THR* 1.3 75.1 - - - +
123B GLU* 1.3 54.5 + - - +
125B THR* 3.1 5.4 + - - -
126B LEU* 2.7 36.9 + - + +
190B LEU* 4.0 19.6 - - + +
194B LYS* 6.1 3.1 - - + -
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.7 12.8 + - - +
118B VAL 3.8 5.2 + - - +
119B THR 3.5 21.3 - - - +
120B LYS* 2.8 13.7 + - - +
122B MET* 1.3 69.2 - - - +
124B ASP* 1.3 51.7 + - - +
125B THR 2.6 6.2 + - - -
126B LEU* 2.5 47.0 + - - +
127B MET* 2.5 37.7 + - + +
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Residues in contact with ASP 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 2.7 15.0 + - - +
121B THR* 3.5 15.2 - - - +
123B GLU* 1.3 71.8 - - - +
125B THR* 1.3 54.4 + - - +
127B MET* 4.0 9.2 - - - +
128B THR* 2.8 25.8 + - - -
186B LYS* 2.7 30.1 + - - -
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.6 25.4 - - + -
121B THR 3.4 7.0 + - - -
122B MET 3.1 9.1 + - - -
123B GLU 2.6 4.0 + - - -
124B ASP* 1.3 73.7 - - - +
126B LEU* 1.3 61.7 + - - +
127B MET 3.0 5.3 + - - -
128B THR* 3.3 4.2 + - - -
129B VAL* 3.1 28.9 + - + +
183B VAL* 5.5 1.0 - - - +
186B LYS* 3.9 23.2 + - + +
187B LEU* 4.0 24.2 - - + +
190B LEU* 3.4 24.5 - - + +
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Residues in contact with LEU 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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34B ILE* 5.0 2.9 - - + -
37B LEU* 4.7 18.8 - - + +
38B ARG* 3.9 42.2 + - + +
41B LYS* 3.4 42.4 - - + +
122B MET* 2.7 16.4 + - + +
123B GLU* 2.5 21.6 + - - +
125B THR* 1.3 72.7 - - - +
127B MET* 1.3 55.7 + - - -
129B VAL* 3.6 16.9 - - + +
130B LYS* 3.5 17.2 - - + +
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Residues in contact with MET 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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123B GLU* 2.5 37.8 + - + +
124B ASP* 4.0 8.3 - - - +
126B LEU* 1.3 71.8 - - - +
128B THR* 1.3 57.5 + - - +
129B VAL 2.9 4.7 - - - -
130B LYS* 2.8 32.4 + - + +
131B GLN* 3.1 22.1 + - + +
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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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124B ASP* 2.8 19.0 + - - -
125B THR 3.3 5.1 + - - -
127B MET* 1.3 76.9 - - - +
129B VAL* 1.3 57.8 + - - +
131B GLN* 3.6 22.7 + - - +
132B TYR* 3.0 23.7 + - - +
179B LEU* 4.8 8.2 - - + +
182B ASP* 2.8 46.5 - - + +
183B VAL* 4.6 0.9 - - - -
186B LYS* 2.8 22.0 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.4 39.7 - - + -
37B LEU* 5.3 0.7 - - + -
38B ARG* 4.0 13.0 - - - +
125B THR* 3.1 24.5 - - + +
126B LEU* 3.6 15.3 - - + +
128B THR* 1.3 76.7 - - - +
130B LYS* 1.3 54.7 + - - +
131B GLN 3.1 0.2 - - - -
132B TYR* 2.9 14.8 + - + +
133B GLU* 2.5 60.5 + - + +
183B VAL* 3.8 10.1 - - + +
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Residues in contact with LYS 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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38B ARG* 5.7 1.8 - - - +
126B LEU* 3.5 15.7 - - + +
127B MET* 2.8 17.4 + - + +
129B VAL* 1.3 80.3 - - - +
131B GLN* 1.3 51.5 + - + +
133B GLU* 3.3 29.3 + - - +
134B ALA* 2.8 33.6 + - - +
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Residues in contact with GLN 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 MET* 3.1 21.5 + - + +
128B THR* 3.6 31.4 + - - +
129B VAL 3.1 0.2 - - - -
130B LYS* 1.3 77.4 - - + +
132B TYR* 1.3 61.0 + - - +
134B ALA* 3.4 19.0 + - - +
135B ALA* 3.5 2.4 + - - +
179B LEU* 2.8 35.0 - - + +
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Residues in contact with TYR 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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27B ASP* 2.7 27.0 + - - -
30B LEU* 3.9 13.5 - - + -
31B GLU* 2.9 18.1 + - - -
34B ILE* 5.4 4.7 - - + -
128B THR 3.0 15.3 + - - +
129B VAL* 2.9 19.0 + - + +
131B GLN* 1.3 78.8 - - - +
133B GLU* 1.3 65.8 + - + +
135B ALA 3.1 16.8 - - - +
136B ARG* 2.9 44.9 - - + +
176B TYR* 4.5 4.9 - + - -
179B LEU* 3.8 14.6 - - + +
180B ARG* 3.0 38.1 + - - -
183B VAL* 4.0 27.8 - - + -
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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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34B ILE* 5.1 1.0 - - - +
38B ARG* 3.0 34.9 + - - -
129B VAL* 2.5 36.8 + - + +
130B LYS* 3.2 32.0 + - - +
132B TYR* 1.3 71.2 - - + +
134B ALA* 1.3 69.8 + - - +
136B ARG* 3.0 53.1 + - - +
137B LEU* 3.4 12.3 - - - +
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Residues in contact with ALA 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 LYS 2.8 13.6 + - - +
131B GLN* 3.4 14.6 - - - +
133B GLU* 1.3 81.5 - - - +
135B ALA* 1.3 59.2 + - + +
136B ARG 3.1 3.3 + - - -
137B LEU* 5.3 0.3 - - - +
138B GLU* 3.5 14.6 + - - +
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Residues in contact with ALA 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 GLN 3.5 1.2 + - - +
132B TYR* 3.1 10.2 + - - +
134B ALA* 1.3 76.4 - - + +
136B ARG* 1.3 55.3 + - - +
138B GLU* 3.4 24.9 - - - +
176B TYR* 2.9 37.3 - - + +
179B LEU* 4.3 19.2 - - + +
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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