Contacts of the helix formed by residues 124 - 136 (chain A) in PDB entry 5E63
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 THR 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A THR* 3.9 5.9 - - - +
120A LYS 4.7 1.7 + - - -
121A GLU* 2.8 33.5 - - + +
122A HIS 3.1 2.0 + - - +
123A LEU* 1.3 77.3 + - - +
125A GLN* 1.3 58.8 + - - +
126A ARG* 3.4 9.0 - - + +
127A GLY* 3.2 21.5 - - - +
128A LEU* 3.0 27.5 + - - +
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Residues in contact with GLN 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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35A THR* 4.4 19.0 - - - +
124A THR* 1.3 70.7 + - - +
126A ARG* 1.3 72.1 + - - +
128A LEU* 3.5 19.9 + - - +
129A GLU* 3.3 48.8 + - - +
150A PHE* 4.6 7.1 - - - -
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Residues in contact with ARG 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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121A GLU* 5.7 2.9 - - - +
124A THR* 3.4 6.9 - - + +
125A GLN* 1.3 81.3 - - - +
127A GLY* 1.3 57.3 + - - +
129A GLU* 3.1 27.2 + - - +
130A LYS* 2.9 45.7 + - + +
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Residues in contact with GLY 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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116A LEU* 5.0 2.6 - - - +
121A GLU* 3.4 32.9 - - - +
124A THR* 3.2 6.7 - - - +
126A ARG* 1.3 75.2 - - - +
128A LEU* 1.3 62.5 + - - -
130A LYS* 3.1 13.9 + - - +
131A ILE* 2.9 33.2 + - - +
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Residues in contact with LEU 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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27A VAL* 3.9 28.5 - - + -
35A THR* 3.7 21.3 - - + +
37A TRP* 3.5 34.1 - - + -
39A VAL* 3.9 20.0 - - + -
121A GLU 4.2 0.6 + - - -
122A HIS 4.5 6.9 + - - +
124A THR 3.0 19.6 + - - +
125A GLN* 3.6 19.5 - - - +
126A ARG 3.2 0.8 - - - -
127A GLY* 1.3 72.2 - - - +
129A GLU* 1.3 51.2 + - - +
131A ILE* 3.1 8.0 + - + +
132A VAL* 2.7 39.1 + - + +
150A PHE* 3.9 15.3 - - + -
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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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125A GLN* 3.3 33.8 + - - +
126A ARG* 3.1 35.5 + - - +
128A LEU* 1.3 75.7 - - - +
130A LYS* 1.3 54.1 + - + +
132A VAL* 3.9 7.2 - - - +
133A SER* 2.7 34.5 + - - -
150A PHE* 4.4 14.0 - - + -
152A GLN* 3.8 29.5 + - - +
153A CYS* 4.9 6.4 - - + +
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Residues in contact with LYS 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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116A LEU* 4.0 22.0 - - + -
121A GLU* 5.0 13.2 - - - +
126A ARG* 2.9 31.9 + - + +
127A GLY* 3.5 10.5 - - - +
129A GLU* 1.3 75.7 - - - +
131A ILE* 1.3 53.4 + - - +
133A SER* 3.1 8.1 + - - -
134A LEU* 2.7 43.5 + - + +
156A THR* 4.8 0.8 - - - +
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Residues in contact with ILE 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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25A VAL* 4.1 11.4 - - + -
27A VAL* 4.0 17.7 - - + -
39A VAL* 4.0 26.9 - - + -
113A VAL* 4.2 15.7 - - + +
116A LEU* 4.3 23.8 - - + -
117A MET* 4.6 3.8 - - + -
122A HIS* 3.5 37.9 - - + +
127A GLY 2.9 18.6 + - - +
128A LEU* 3.5 8.1 - - + +
130A LYS* 1.3 71.6 - - - +
132A VAL* 1.3 60.2 + - - +
134A LEU* 3.8 7.4 - - - +
135A LYS* 2.8 29.6 + - - +
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Residues in contact with VAL 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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27A VAL* 4.3 19.7 - - + -
128A LEU* 2.7 25.0 + - + +
129A GLU* 3.9 7.6 - - - +
131A ILE* 1.3 71.6 - - - +
133A SER* 1.3 64.9 + - - +
135A LYS* 3.4 5.0 + - + +
136A ALA* 3.1 19.8 + - - +
142A LEU* 3.5 20.6 - - + +
146A LEU* 4.8 3.1 - - + -
150A PHE* 3.7 57.9 - - + -
153A CYS* 3.9 12.6 - - + -
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Residues in contact with SER 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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129A GLU 2.7 23.0 + - - -
130A LYS* 3.3 8.3 - - - -
132A VAL* 1.3 74.0 - - - +
134A LEU* 1.3 61.4 + - - +
136A ALA* 3.4 12.3 + - - +
137A SER 4.2 0.9 + - - -
153A CYS* 3.9 14.8 - - - -
154A VAL* 2.4 31.5 + - - +
155A PRO* 3.6 0.2 - - - +
156A THR* 3.0 38.7 + - - +
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Residues in contact with LEU 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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109A LEU* 3.8 21.7 - - + +
112A LYS* 4.2 24.2 - - + -
113A VAL* 3.9 27.1 - - + +
116A LEU* 3.5 30.7 - - + -
130A LYS* 2.7 28.6 + - + +
131A ILE* 3.8 3.6 - - - +
133A SER* 1.3 69.3 - - - +
135A LYS* 1.3 65.8 + - - +
136A ALA 3.1 2.3 + - - -
137A SER* 3.2 14.2 + - - -
138A ILE* 3.3 15.5 - - - +
156A THR* 3.3 26.9 - - + +
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Residues in contact with LYS 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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25A VAL* 3.0 39.6 + - + +
26A ARG* 4.8 0.8 - - - +
27A VAL* 4.0 22.7 - - + +
113A VAL* 5.1 0.6 - - - +
131A ILE 2.8 22.5 + - - +
132A VAL* 3.4 6.7 + - - +
134A LEU* 1.3 71.6 - - - +
136A ALA* 1.3 61.9 + - - +
137A SER 3.2 0.2 - - - -
138A ILE* 3.1 34.5 + - + +
141A GLY* 3.8 20.8 + - - +
142A LEU* 4.2 7.6 - - + +
143A SER* 4.9 4.5 - - - +
146A LEU* 3.5 26.5 - - + -
17C G 4.2 19.2 + - - -
18C A 5.0 9.5 + - - -
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Residues in contact with ALA 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 VAL 3.1 12.2 + - - +
133A SER* 3.4 15.3 - - - +
134A LEU 3.1 1.4 - - - -
135A LYS* 1.3 74.6 - - - +
137A SER* 1.3 56.8 + - - +
138A ILE 3.5 0.2 - - - -
141A GLY* 3.7 13.5 - - - -
142A LEU* 3.6 30.4 + - + +
147A GLN* 5.9 0.4 - - - +
153A CYS* 4.7 2.2 - - - -
155A PRO* 3.9 26.2 - - + +
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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