Contacts of the helix formed by residues 121 - 134 (chain B) in PDB entry 4I06
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 121 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B PHE* 3.4 16.8 - - - -
36B GLY* 3.7 5.3 - - - -
92B VAL* 3.7 21.5 - - - +
96B ASN* 3.0 17.4 + - - -
119B ASP* 2.6 22.8 + - - -
120B HIS* 1.3 76.4 - - - +
122B LEU* 1.3 62.3 + - - +
124B ILE* 3.1 16.6 + - - +
159B LEU* 4.0 8.7 - - - -
160B HIS* 3.7 22.6 - - - +
163B PRO* 4.4 5.2 - - - -
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Residues in contact with LEU 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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31B ALA* 3.8 18.6 - - + +
33B PHE* 3.7 23.3 - - + -
96B ASN* 3.2 10.4 - - - +
99B LEU* 3.6 4.8 - - + +
115B THR* 4.0 10.5 - - + +
117B GLY* 3.4 32.1 - - - +
118B GLY 4.0 2.0 - - - -
119B ASP 3.2 24.0 + - - +
120B HIS 2.9 1.0 - - - -
121B SER* 1.3 80.4 + - - +
123B ALA* 1.3 62.2 + - - +
124B ILE 3.1 0.2 - - - -
125B GLY* 3.0 4.5 + - - -
126B THR* 3.0 41.5 + - + +
293B ASP* 4.3 7.4 - - + +
295B VAL* 3.7 19.5 - - + -
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Residues in contact with ALA 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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120B HIS* 3.1 24.5 + - + +
122B LEU* 1.3 78.1 - - - +
124B ILE* 1.3 66.6 + - - +
126B THR* 3.5 9.9 - - - -
127B ILE* 3.0 30.4 + - + +
141B TRP* 3.6 32.3 - - + -
163B PRO* 4.7 1.6 - - + -
167B LEU* 3.9 2.6 - - + +
249B SER* 3.9 7.6 - - - +
293B ASP* 3.9 5.2 - - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 4.7 3.1 - - + -
96B ASN* 3.8 17.9 - - + +
121B SER* 3.1 20.7 + - - +
123B ALA* 1.3 77.3 - - - +
125B GLY* 1.3 58.0 + - - +
128B SER* 2.8 38.7 + - - +
159B LEU* 5.2 2.5 - - + +
163B PRO* 3.7 30.4 - - + +
166B PHE* 3.9 25.4 - - + -
167B LEU* 4.1 13.2 - - + +
181B PHE* 4.0 16.4 - - + -
183B TRP* 4.4 1.3 - - + -
184B ILE* 3.5 31.6 - - + -
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Residues in contact with GLY 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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96B ASN* 2.9 44.5 + - - -
99B LEU* 4.5 2.7 - - - -
100B ALA* 3.2 19.9 - - - -
122B LEU 3.0 0.4 + - - -
124B ILE* 1.3 76.1 - - - +
126B THR* 1.3 59.7 + - - +
129B GLY* 2.9 23.9 + - - -
183B TRP* 4.4 1.6 - - - -
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Residues in contact with THR 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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99B LEU* 3.6 16.2 - - + -
103B VAL* 3.6 18.0 - - + +
115B THR* 3.5 24.7 - - + +
122B LEU* 3.0 13.7 + - + +
123B ALA* 3.5 8.0 - - - -
125B GLY* 1.3 77.2 - - - +
127B ILE* 1.3 61.0 + - - +
130B HIS* 2.9 30.7 + - - +
247B HIS* 3.3 8.0 - - - -
293B ASP* 2.9 38.3 + - - +
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Residues in contact with ILE 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 ALA* 3.0 17.3 + - + +
126B THR* 1.3 78.2 + - - +
128B SER* 1.3 61.3 + - - +
130B HIS* 3.6 2.5 - - - +
131B ALA* 2.8 29.5 + - - +
137B LEU* 4.4 19.3 - - + -
139B VAL* 4.2 17.0 - - + -
141B TRP* 3.9 22.9 - - + -
167B LEU* 3.7 34.1 - - + -
187B CYS* 4.8 3.6 - - + -
188B ILE* 4.7 11.7 - - + -
193B ILE* 6.3 0.2 - - + -
247B HIS* 3.4 36.3 - - + +
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Residues in contact with SER 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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100B ALA* 4.6 0.7 - - - -
124B ILE* 2.8 26.1 + - - +
125B GLY 3.9 2.5 - - - -
127B ILE* 1.3 79.0 - - - +
129B GLY* 1.3 61.6 + - - +
131B ALA* 3.3 2.3 + - - +
132B ARG* 3.2 28.3 + - - +
167B LEU* 3.9 7.1 - - - +
183B TRP* 3.8 28.4 - - - -
184B ILE* 4.6 6.4 - - - +
185B LYS 5.0 0.5 + - - -
187B CYS* 3.8 22.7 - - - -
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Residues in contact with GLY 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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100B ALA* 3.3 28.8 - - - +
103B VAL* 4.0 7.0 - - - -
104B SER* 3.5 17.5 - - - -
107B VAL* 5.4 0.2 - - - +
125B GLY 2.9 14.5 + - - -
126B THR 3.9 0.9 - - - -
128B SER* 1.3 76.9 - - - +
130B HIS* 1.3 61.8 + - - +
132B ARG* 3.4 19.6 + - - +
133B HIS* 4.3 1.9 + - - -
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Residues in contact with HIS 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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103B VAL* 3.7 10.4 - - + +
107B VAL* 4.1 14.4 - - + +
126B THR 2.9 18.7 + - - +
127B ILE 3.6 4.0 - - - +
129B GLY* 1.3 76.2 - - - +
131B ALA* 1.3 62.7 + - - +
132B ARG 3.2 0.7 + - - -
133B HIS* 3.5 3.1 + - - +
134B CYS* 3.1 37.8 + - + +
137B LEU* 3.5 15.6 - - + +
245B PRO* 4.3 0.8 - - - +
246B ILE 3.9 9.9 - - - -
247B HIS* 2.9 29.1 + - + +
290B SER* 2.7 36.9 + - - -
291B ALA* 3.4 20.3 - - + +
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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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127B ILE* 2.8 19.7 + - + +
128B SER 3.9 4.3 - - - +
129B GLY 3.3 0.4 - - - -
130B HIS* 1.3 75.5 - - - +
132B ARG* 1.3 64.8 + - - +
134B CYS 3.7 6.1 - - - +
135B PRO* 3.3 28.8 - - + +
137B LEU* 3.6 17.7 - - + +
187B CYS* 3.9 26.5 - - + +
188B ILE* 5.2 0.9 - - + -
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Residues in contact with ARG 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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97B GLN* 5.0 4.9 + - - +
100B ALA* 3.7 30.7 + - - +
101B GLU* 3.6 27.0 + - - +
104B SER* 3.8 18.4 - - - +
128B SER* 3.2 16.9 + - - +
129B GLY* 3.5 10.5 - - - +
130B HIS 3.1 1.2 - - - -
131B ALA* 1.3 78.6 - - - +
133B HIS* 1.3 65.5 + - + +
135B PRO* 4.7 3.3 - - - +
183B TRP* 3.8 32.3 - - - -
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Residues in contact with HIS 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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104B SER* 2.9 49.7 + - - -
107B VAL* 4.3 8.1 - - + -
108B SER* 3.5 24.7 - - - -
129B GLY 4.5 1.6 - - - -
130B HIS 3.5 2.0 + - - -
132B ARG* 1.3 83.4 + - + +
134B CYS* 1.3 71.8 + - - +
135B PRO* 3.4 11.2 - - - +
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Residues in contact with CYS 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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107B VAL* 3.5 32.1 - - - -
130B HIS* 3.1 24.7 + - + +
131B ALA* 3.6 3.4 - - - -
133B HIS* 1.3 84.3 - - - +
135B PRO* 1.3 65.1 - - - +
136B ASP 3.2 2.7 - - - -
137B LEU* 3.0 24.4 + - - +
245B PRO* 3.8 23.6 - - + -
290B SER* 4.4 4.9 - - - -
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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