Contacts of the helix formed by residues 126 - 135 (chain A) in PDB entry 3EU9
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A HIS* 3.5 2.0 - - - -
117A ASP* 3.3 32.5 + - - +
118A GLN 3.5 2.0 - - - -
119A LEU* 3.5 16.4 - - + -
125A SER* 1.3 75.3 - - - +
127A PRO* 1.3 76.6 - - - +
128A LEU* 3.4 8.4 + - - +
129A HIS* 3.0 44.2 + - + +
130A TRP* 3.1 13.7 + - - -
149A ASP 5.5 1.0 + - - -
152A LEU* 4.0 21.8 - - + +
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Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 4.6 0.7 - - - +
94A LEU* 4.0 36.8 - - + +
95A HIS* 3.6 27.4 - - + +
98A ALA* 3.7 11.9 - - + +
115A ILE 4.8 1.6 - - - +
116A VAL 3.3 26.7 - - - +
118A GLN* 3.3 14.4 - - + +
126A THR* 1.3 86.2 - - - +
128A LEU* 1.3 56.4 + - - +
130A TRP* 3.2 4.7 + - + +
131A ALA* 2.9 28.2 + - - +
143A LEU* 3.9 9.2 - - + -
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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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116A VAL 5.3 0.4 + - - -
117A ASP* 4.7 2.0 + - - +
126A THR* 3.1 8.3 + - - +
127A PRO* 1.3 77.3 - - - +
129A HIS* 1.3 55.9 + - - +
131A ALA* 3.3 1.0 + - + +
132A THR* 2.7 43.8 + - - +
140A VAL* 3.9 39.9 - - + +
143A LEU* 3.6 17.8 - - + +
144A MET* 4.1 3.8 - - + -
148A ALA* 3.8 28.3 - - + +
149A ASP 3.9 3.8 - - - +
150A PRO* 3.7 42.0 - - + -
160A CYS* 3.6 9.9 - - - -
176A LEU* 6.2 0.2 - - + -
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.8 0.2 - - + -
125A SER* 3.6 21.8 - - - -
126A THR* 3.0 45.5 + - + +
128A LEU* 1.3 75.4 - - - +
130A TRP* 1.3 60.1 + - - +
132A THR* 3.2 2.3 + - - -
133A ARG* 2.9 35.8 + - - +
149A ASP 5.4 0.9 - - - -
152A LEU* 2.9 39.8 + - + +
153A ILE 3.6 14.5 + - - -
154A ASP* 3.9 5.6 - - + -
158A CYS 3.8 11.9 - - - -
160A CYS* 3.7 22.0 + - - -
163A LEU* 3.7 21.4 - - + +
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Residues in contact with TRP 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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91A VAL* 3.5 45.5 - - + -
95A HIS* 3.6 34.9 - + + +
96A TRP* 4.1 27.4 - + - -
99A ILE* 3.7 33.6 - - + +
120A GLY 4.5 3.0 + - - -
121A GLY* 4.4 11.2 - - - -
122A ASP 5.7 0.2 - - - -
123A LEU* 5.8 3.4 - - - +
125A SER* 3.7 23.3 + - - -
126A THR 3.1 14.4 + - - +
127A PRO* 3.2 10.5 + - + +
129A HIS* 1.3 81.0 - - - +
131A ALA* 1.3 62.1 + - - +
133A ARG* 3.3 13.8 + - - +
134A GLN* 3.0 26.1 + - - +
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Residues in contact with ALA 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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98A ALA* 4.2 12.0 - - + +
127A PRO 2.9 15.0 + - - +
128A LEU* 3.7 5.8 - - - +
130A TRP* 1.3 77.2 - - - +
132A THR* 1.3 57.7 + - - +
134A GLN* 3.8 4.0 - - - +
135A GLY 2.9 22.0 + - - -
136A HIS* 3.0 15.1 + - + +
139A MET* 3.6 35.0 - - + -
140A VAL* 4.3 9.9 - - + -
143A LEU* 4.3 5.4 - - + -
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Residues in contact with THR 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 LEU* 2.7 25.0 + - - +
129A HIS* 3.5 5.6 - - - -
131A ALA* 1.3 75.2 - - - +
133A ARG* 1.3 66.1 + - - +
135A GLY* 3.0 10.6 + - - -
140A VAL* 3.7 18.8 - - - +
160A CYS* 3.4 45.3 - - + +
163A LEU* 3.9 6.1 - - + -
164A ALA* 3.7 21.5 - - + +
169A HIS* 3.0 16.1 - - - -
172A ILE* 4.1 10.4 - - + +
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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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99A ILE* 6.2 1.6 - - + -
123A LEU* 3.8 26.0 - - - +
125A SER* 4.9 5.7 + - - -
129A HIS* 2.9 21.9 + - - +
130A TRP* 3.7 13.0 - - - +
132A THR* 1.3 75.4 - - - +
134A GLN* 1.3 55.6 + - - +
154A ASP* 3.4 22.2 + - - -
156A GLU* 3.1 26.7 + - - -
158A CYS* 5.9 0.4 - - - -
163A LEU* 3.8 25.6 - - + +
166A GLN* 5.1 2.4 - - - +
167A PHE* 3.5 52.2 - - + +
169A HIS* 2.7 23.4 + - - -
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Residues in contact with GLN 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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99A ILE* 3.6 30.4 - - + +
130A TRP 3.0 17.1 + - - +
131A ALA 3.9 3.4 - - - +
133A ARG* 1.3 78.4 - - - +
135A GLY* 1.3 59.8 + - - +
136A HIS* 3.2 35.0 + - + +
169A HIS* 3.7 7.4 - - - -
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Residues in contact with GLY 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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131A ALA 2.9 4.8 + - - -
132A THR 3.0 14.3 + - - -
133A ARG 3.1 0.4 - - - -
134A GLN* 1.3 80.7 - - - +
136A HIS* 1.3 63.9 + - - +
137A LEU* 3.4 6.4 + - - +
169A HIS* 3.5 20.4 + - - -
172A ILE* 3.7 11.2 - - - +
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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