Contacts of the helix formed by residues 126 - 138 (chain A) in PDB entry 4OUH
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 ASN 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ASP* 2.9 31.2 + - - +
111A TYR* 3.9 9.1 - - + -
125A LYS* 1.3 77.1 - - - +
127A SER* 1.3 64.6 + - - +
128A GLU* 3.3 3.4 - - - -
129A GLU* 3.2 18.9 + - + +
130A LEU* 2.9 19.9 + - - +
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Residues in contact with SER 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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25A PHE* 4.0 14.4 - - - -
124A TYR* 3.5 30.1 + - - +
125A LYS 4.0 2.2 - - - -
126A ASN* 1.3 76.3 - - - +
128A GLU* 1.3 60.6 + - - +
130A LEU* 3.2 8.2 + - - +
131A ARG* 2.8 38.2 + - - +
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Residues in contact with GLU 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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126A ASN 3.3 0.6 - - - -
127A SER* 1.3 77.8 - - - +
129A GLU* 1.3 64.4 + - - +
131A ARG* 3.0 40.6 + - - +
132A SER* 3.1 23.4 + - - -
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Residues in contact with GLU 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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110A ASP* 5.5 1.7 - - - +
111A TYR* 2.7 31.5 + - + +
126A ASN* 3.2 23.9 + - + +
128A GLU* 1.3 76.2 - - - +
130A LEU* 1.3 61.2 + - - +
132A SER* 3.2 5.9 + - - -
133A ARG* 2.8 47.6 + - + +
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Residues in contact with LEU 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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22A LEU* 4.0 16.2 - - + -
25A PHE* 3.5 42.0 - - + -
106A LEU* 3.9 33.0 - - + -
111A TYR* 3.8 36.9 - - + -
124A TYR* 4.8 7.4 - - + -
125A LYS 5.2 1.3 - - - +
126A ASN 2.9 13.2 + - - +
127A SER* 3.2 10.5 + - - +
129A GLU* 1.3 76.1 - - - +
131A ARG* 1.3 61.6 + - - +
133A ARG* 3.3 2.2 + - - +
134A ILE* 2.9 35.8 + - + +
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Residues in contact with ARG 131 (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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-1A SER 3.4 23.8 + - - -
0A PRO* 3.8 14.1 - - - +
1A MET* 3.4 24.2 - - + +
25A PHE* 3.6 17.3 - - + -
29A GLU* 3.3 21.5 + - - +
127A SER* 2.8 24.9 + - - +
128A GLU* 3.0 39.9 + - - +
130A LEU* 1.3 72.5 - - - +
132A SER* 1.3 58.6 + - - +
134A ILE* 3.4 0.9 + - - +
135A VAL* 2.9 38.1 + - + +
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Residues in contact with SER 132 (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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128A GLU 3.1 16.0 + - - -
129A GLU* 3.5 7.0 - - - -
131A ARG* 1.3 79.3 - - - +
133A ARG* 1.3 59.1 + - - +
135A VAL* 3.8 4.5 - - - +
136A SER* 2.8 40.6 + - - -
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Residues in contact with ARG 133 (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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104A LEU* 3.5 27.3 - - + +
105A THR 2.9 25.5 + - - +
106A LEU* 3.7 20.7 - - + +
107A ASN 5.2 0.8 - - - +
111A TYR* 2.9 34.2 + - - -
129A GLU* 2.8 35.8 + - + +
130A LEU* 3.9 3.8 - - - +
132A SER* 1.3 72.7 - - - +
134A ILE* 1.3 57.9 + - - +
136A SER* 4.1 4.0 - - - -
137A GLY* 2.6 32.9 + - - -
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Residues in contact with ILE 134 (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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22A LEU* 5.4 2.0 - - + -
25A PHE* 3.9 29.2 - - + -
26A LEU* 3.9 36.8 - - + -
29A GLU* 3.9 22.7 - - + -
91A LEU* 4.8 0.4 - - + -
104A LEU* 3.9 16.4 - - + -
106A LEU* 4.4 8.1 - - + -
130A LEU* 2.9 35.6 + - + +
131A ARG 3.9 2.2 - - - +
133A ARG* 1.3 74.1 - - - +
135A VAL* 1.3 58.5 + - - +
138A ILE* 2.7 42.2 + - + +
139A ILE* 3.2 7.7 + - + -
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Residues in contact with VAL 135 (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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29A GLU* 3.7 21.8 - - - +
33A HIS* 3.8 21.1 - - + +
131A ARG* 2.9 23.5 + - + +
132A SER* 3.9 4.7 - - - +
134A ILE* 1.3 77.4 - - - +
136A SER* 1.3 61.9 + - - +
139A ILE* 3.4 13.6 + - + -
140A THR* 2.9 45.4 + - - +
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Residues in contact with SER 136 (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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132A SER* 2.8 29.9 + - - -
133A ARG* 4.1 3.4 - - - -
135A VAL* 1.3 74.5 - - - +
137A GLY* 1.3 58.7 - - - +
140A THR* 4.5 6.0 - - - -
141A PRO* 3.2 21.5 - - - +
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Residues in contact with GLY 137 (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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102A ALA* 3.2 22.7 - - - +
103A ASP 4.5 4.9 + - - +
104A LEU* 4.5 13.9 - - - -
133A ARG 2.6 23.2 + - - -
136A SER* 1.3 75.8 - - - +
138A ILE* 1.3 64.6 + - - +
141A PRO* 3.5 6.2 - - - +
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Residues in contact with ILE 138 (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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26A LEU* 5.0 7.2 - - + -
30A VAL* 5.4 3.6 - - + -
78A LEU* 6.0 0.4 - - + -
91A LEU* 4.4 17.7 - - + +
93A VAL* 3.5 31.0 - - + -
102A ALA* 3.9 22.5 - - + +
104A LEU* 4.0 29.2 - - + -
134A ILE* 2.7 26.8 + - + +
137A GLY* 1.3 85.8 - - - +
139A ILE* 1.3 75.8 + - + +
140A THR 3.5 1.1 - - - -
141A PRO* 3.2 9.3 - - - +
142A ILE* 3.2 31.9 + - + +
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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