Contacts of the helix formed by residues 117 - 130 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.0 9.0 + - - +
116A VAL* 1.3 91.7 + - - +
118A VAL* 1.3 62.1 + - - +
119A MET 3.1 2.5 - - - -
120A ASP* 2.8 32.3 + - - +
121A ILE* 3.1 14.2 + - - +
117B ASP* 4.1 15.0 - - + +
120B ASP* 3.1 42.1 - - - +
121B ILE* 3.7 14.7 + - + +
124B GLU* 4.7 7.1 - - - +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 3.5 21.1 - - - +
100A VAL* 5.0 2.7 - - + -
115A ASP* 2.9 22.8 + - - +
117A ASP* 1.3 75.9 - - - +
119A MET* 1.3 62.8 + - - +
121A ILE* 3.1 12.2 + - + +
122A ALA* 3.1 20.0 + - + +
136A ILE* 3.9 37.0 - - + +
138A VAL* 3.8 25.4 - - + -
121B ILE* 3.8 15.9 - - + -
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Residues in contact with MET 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 4.7 10.1 - - + -
39A ILE* 3.5 36.3 - - + +
94A PHE* 4.0 24.9 - - + +
96A GLY 4.4 16.6 - - - +
97A HIS* 6.2 0.7 - - - -
98A GLN* 4.6 9.8 + - - +
115A ASP* 4.6 0.2 + - - -
116A VAL* 4.1 12.0 + - - +
117A ASP 3.1 0.4 - - - -
118A VAL* 1.3 79.7 - - - +
120A ASP* 1.3 63.4 + - - +
122A ALA* 3.4 14.0 + - + +
123A LYS* 3.1 21.1 + - - +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A VAL* 4.3 8.0 - - - +
117A ASP* 2.8 25.7 + - - +
119A MET* 1.3 73.0 - - - +
121A ILE* 1.3 60.5 + - - +
123A LYS* 3.2 23.7 + - - +
124A GLU* 2.9 32.4 + - + +
117B ASP* 3.2 25.7 - - - +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP 3.1 7.7 + - - +
118A VAL* 3.1 18.9 + - + +
120A ASP* 1.3 76.5 - - - +
122A ALA* 1.3 58.5 + - - +
124A GLU* 3.2 5.8 + - - +
125A ALA* 2.9 28.1 + - - +
136A ILE* 3.7 18.8 - - + -
138A VAL* 5.5 0.4 - - + -
100B VAL* 5.5 0.7 - - + -
113B PHE* 3.7 25.7 - - + -
115B ASP* 3.6 17.5 - - - +
117B ASP* 3.8 10.1 - - + -
118B VAL* 3.6 28.0 - - + -
121B ILE* 3.9 21.5 - - + -
138B VAL* 4.8 12.6 - - + -
140B ALA* 5.5 0.2 - - + -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL 3.1 11.8 + - - +
119A MET* 3.5 21.1 - - + +
121A ILE* 1.3 75.9 - - - +
123A LYS* 1.3 57.5 + - - +
125A ALA* 3.4 0.7 + - - -
126A HIS* 3.0 26.2 + - - +
133A VAL* 3.5 30.1 - - + +
136A ILE* 3.6 16.4 - - + +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR 6.1 0.9 - - - +
44A HIS* 6.0 4.0 + - - -
119A MET 3.1 13.6 + - - +
120A ASP* 3.5 25.7 + - - +
121A ILE 3.2 0.4 - - - -
122A ALA* 1.3 73.8 - - - +
124A GLU* 1.3 61.3 + - + +
126A HIS* 3.2 6.6 + - - +
127A GLU* 2.9 54.2 + - + +
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Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 2.9 19.1 + - + +
121A ILE* 3.7 5.2 - - - +
123A LYS* 1.3 76.6 - - + +
125A ALA* 1.3 63.6 + - - +
127A GLU* 3.4 18.6 + - - +
128A GLN* 3.0 59.8 + - - +
3B ILE* 5.3 3.1 - - - +
113B PHE* 4.2 5.4 - - + -
114B MET 4.3 8.3 - - - +
115B ASP* 5.7 3.6 - - - +
116B VAL* 5.7 8.0 - - + +
117B ASP* 4.3 12.3 - - - +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE 2.9 16.3 + - - +
122A ALA* 3.6 5.6 - - - +
124A GLU* 1.3 76.5 - - - +
126A HIS* 1.3 61.3 + - - +
129A THR* 2.9 33.3 + - - +
133A VAL* 3.8 17.0 - - + -
102B VAL* 4.2 8.1 - - + -
113B PHE* 3.6 38.0 - - + -
140B ALA* 4.9 2.9 - - + -
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Residues in contact with HIS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 3.7 47.2 + - + +
122A ALA 3.0 15.6 + - - +
123A LYS* 3.2 6.5 + - - +
125A ALA* 1.3 76.6 - - - +
127A GLU* 1.3 68.5 + - + +
130A GLY* 2.7 45.3 + - - -
131A TYR 2.9 30.8 + - - +
132A LYS* 4.4 2.4 + - + -
133A VAL* 4.3 4.4 - - + +
148B GLN* 5.4 4.5 - - - -
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LYS* 2.9 43.2 + - + +
124A GLU* 3.6 28.9 - - - +
126A HIS* 1.3 87.0 - - + +
128A GLN* 1.3 61.4 + - + +
130A GLY 4.6 0.9 + - - -
3B ILE* 6.0 2.0 - - + +
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Residues in contact with GLN 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLU* 3.0 41.8 + - - +
127A GLU* 1.3 79.7 - - + +
129A THR* 1.3 59.3 + - - +
3B ILE* 3.9 42.7 - - + +
4B HIS 5.1 1.0 - - - +
112B ASP 5.3 1.1 - - - +
113B PHE* 3.5 13.9 - - + +
114B MET* 2.8 56.6 + - - +
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Residues in contact with THR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ALA 2.9 22.4 + - - +
128A GLN* 1.3 79.8 - - - +
130A GLY* 1.3 59.7 + - - +
131A TYR* 3.1 41.9 + - + +
102B VAL* 4.2 13.2 - - + -
111B ALA* 3.0 29.3 - - - +
112B ASP 4.2 9.9 + - - -
113B PHE* 5.0 1.8 - - - -
145B PRO* 3.7 13.3 - - - +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A HIS* 2.7 36.1 + - - -
127A GLU 4.5 1.0 + - - -
128A GLN 3.8 0.4 - - - -
129A THR* 1.3 71.8 - - - +
131A TYR* 1.3 64.3 + - - +
145B PRO* 3.8 12.4 - - - +
148B GLN* 3.0 16.3 + - - -
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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