Contacts of the helix formed by residues 117 - 130 (chain B) in PDB entry 4I7H
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 ASP 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ASP* 4.1 14.8 - - + +
120A ASP* 3.2 40.6 - - - +
121A ILE* 3.8 13.4 + - + -
124A GLU* 4.3 10.6 - - - +
115B ASP* 2.9 9.9 + - - +
116B VAL* 1.3 90.9 + - - +
118B VAL* 1.3 66.1 + - - +
119B MET 3.2 2.2 - - - -
120B ASP* 3.1 24.9 + - - +
121B ILE* 3.4 14.3 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.6 23.6 - - + -
98B GLN* 3.4 26.0 - - - +
100B VAL* 5.5 0.7 - - + -
115B ASP* 3.2 15.9 + - - +
117B ASP* 1.3 76.8 - - - +
119B MET* 1.3 63.1 + - - +
121B ILE* 3.0 20.3 + - + +
122B ALA* 3.2 11.3 + - + +
136B ILE* 4.0 36.8 - - + +
138B VAL* 4.0 17.0 - - + -
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 4.0 20.4 - - + -
38B MET 6.0 0.2 - - - +
39B ILE* 3.6 40.2 - - + +
94B PHE* 4.0 31.0 - - + +
95B MET* 5.3 3.8 - - - -
96B GLY 4.5 11.0 - - - +
115B ASP* 4.9 0.2 + - - -
116B VAL* 4.2 13.4 + - - +
117B ASP 3.2 0.4 - - - -
118B VAL* 1.3 77.7 - - - +
120B ASP* 1.3 66.5 + - - +
121B ILE 3.2 0.2 + - - -
122B ALA* 3.3 11.5 + - - +
123B LYS* 3.2 39.4 + - - +
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 3.1 27.3 - - - +
116B VAL 4.7 7.9 - - - +
117B ASP* 3.1 16.7 + - - +
119B MET* 1.3 80.2 - - - +
121B ILE* 1.3 57.1 + - - +
123B LYS* 3.9 18.5 + - - +
124B GLU* 3.1 28.8 + - + +
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Residues in contact with ILE 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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100A VAL* 5.4 0.4 - - + -
113A PHE* 3.6 27.5 - - + -
115A ASP* 3.6 14.1 - - - +
117A ASP* 3.7 9.6 - - + -
118A VAL* 3.8 28.0 - - + -
121A ILE* 3.9 21.3 - - + -
138A VAL* 4.9 11.4 - - + -
117B ASP 3.5 13.0 - - - +
118B VAL* 3.0 14.8 + - + +
120B ASP* 1.3 78.0 - - - +
122B ALA* 1.3 60.0 + - - +
124B GLU* 3.3 5.2 + - - +
125B ALA* 2.8 29.3 + - - +
136B ILE* 3.9 17.3 - - + -
138B VAL* 5.9 0.2 - - + -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 3.2 7.0 + - + +
119B MET* 3.6 13.9 - - - +
121B ILE* 1.3 80.4 - - - +
123B LYS* 1.3 57.8 + - + +
126B HIS* 3.0 24.8 + - - +
133B VAL* 3.5 28.7 - - + +
136B ILE* 3.6 21.4 - - + +
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Residues in contact with LYS 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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41B SER 5.3 5.2 - - - -
42B THR 4.4 16.8 - - - +
43B GLU 5.4 0.2 - - - -
44B HIS* 3.5 24.1 + - + +
93B ASP* 2.9 27.2 + - - -
94B PHE 4.3 8.1 + - - -
95B MET* 5.9 0.4 - - - +
119B MET* 3.2 32.7 + - - +
120B ASP* 4.0 20.2 + - - +
121B ILE 3.2 0.4 - - - -
122B ALA* 1.3 76.0 - - + +
124B GLU* 1.3 66.8 + - - +
126B HIS* 3.1 6.1 + - - +
127B GLU* 2.9 40.3 + - + +
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Residues in contact with GLU 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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3A ILE* 4.4 7.3 - - - +
113A PHE* 4.2 4.7 - - + -
114A MET 4.4 9.4 - - - +
115A ASP* 5.8 3.8 - - - +
116A VAL* 6.1 5.2 - - + +
117A ASP* 4.7 6.7 - - - +
120B ASP* 3.1 22.4 + - + +
121B ILE* 3.3 5.6 + - - +
123B LYS* 1.3 75.1 - - - +
125B ALA* 1.3 61.3 + - - +
127B GLU* 3.5 26.0 + - - +
128B GLN* 3.0 62.3 + - - +
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Residues in contact with ALA 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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102A VAL* 4.1 9.2 - - + -
113A PHE* 3.7 36.0 - - + -
140A ALA* 4.9 3.6 - - + -
121B ILE 2.8 17.8 + - - +
122B ALA* 3.7 6.1 - - - +
124B GLU* 1.3 78.5 - - - +
126B HIS* 1.3 62.4 + - - +
128B GLN* 4.0 0.2 - - - -
129B THR* 2.9 32.2 + - + +
133B VAL* 4.0 13.7 - - + -
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Residues in contact with HIS 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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148A GLN* 5.8 1.6 - - - -
42B THR* 3.0 51.7 + - + +
122B ALA 3.0 18.6 + - - +
123B LYS* 3.1 4.9 + - - +
125B ALA* 1.3 76.9 - - - +
127B GLU* 1.3 70.1 + - + +
130B GLY* 3.0 33.8 + - - +
131B TYR 2.6 30.6 + - - +
132B LYS* 4.1 4.5 - - + -
133B VAL* 4.2 5.1 + - + +
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Residues in contact with GLU 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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3A ILE* 5.7 3.6 - - + +
123B LYS* 2.9 28.8 + - + +
124B GLU* 3.7 30.5 - - - +
126B HIS* 1.3 85.3 - - + +
128B GLN* 1.3 60.4 + - + +
130B GLY 4.8 0.5 + - - -
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Residues in contact with GLN 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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3A ILE* 3.5 45.7 - - + +
4A HIS 4.9 1.4 - - - +
112A ASP 5.4 2.4 - - - +
113A PHE* 3.5 15.8 - - + +
114A MET* 2.8 47.6 + - - +
124B GLU* 3.0 38.6 + - - +
126B HIS 3.3 0.2 - - - -
127B GLU* 1.3 79.7 - - + +
129B THR* 1.3 58.2 + - - +
130B GLY 3.8 0.2 - - - -
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 4.6 11.6 - - + +
111A ALA* 3.2 31.4 - - - +
112A ASP 4.3 8.8 + - - -
113A PHE* 5.1 1.8 - - - -
145A PRO* 3.7 9.5 - - - +
125B ALA* 2.9 24.3 + - - +
128B GLN* 1.3 81.5 - - - +
130B GLY* 1.3 60.6 - - - +
131B TYR* 3.1 45.8 + - + +
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Residues in contact with GLY 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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145A PRO* 3.8 14.2 - - - +
148A GLN* 3.1 16.8 + - - -
126B HIS* 3.0 26.3 + - - -
127B GLU 4.7 0.8 + - - -
128B GLN 3.8 0.2 - - - -
129B THR* 1.3 77.7 - - - +
131B TYR* 1.3 65.4 + - - +
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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