Contacts of the helix formed by residues 129 - 136 (chain A) in PDB entry 3QEO
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 SER 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.5 10.1 - - - -
27A GLU* 2.6 22.7 + - - -
104A MET* 3.4 11.2 - - - +
108A GLN* 4.3 3.8 - - - +
126A PHE* 5.6 1.6 - - - -
128A ARG* 1.3 76.8 - - - +
130A VAL* 1.3 60.1 + - - +
131A TYR* 3.0 26.0 + - - +
132A SER* 3.1 18.5 + - - -
133A ALA* 2.9 28.9 + - - +
172A LEU* 4.5 3.4 - - - -
215A TRP* 3.8 1.6 - - - -
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Residues in contact with VAL 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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101A CYS* 5.0 6.7 - - + +
104A MET* 3.5 21.0 - - + -
105A ILE* 3.9 21.1 - - + -
108A GLN* 4.5 9.3 + - - +
129A SER* 1.3 74.4 - - - +
131A TYR* 1.3 85.4 + - + +
133A ALA* 3.7 5.4 - - - +
134A ARG 3.1 15.2 + - - -
159A HIS* 2.7 31.1 + - + +
163A ASN* 3.4 34.8 - - - +
170A LEU* 5.4 4.5 - - + -
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Residues in contact with TYR 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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129A SER* 3.0 18.6 - - - +
130A VAL* 1.3 95.8 - - + +
132A SER* 1.3 60.0 + - - +
134A ARG* 4.8 0.4 - - - -
135A TYR* 2.7 44.8 + + + +
163A ASN* 6.1 0.2 - - + -
167A GLY 5.5 1.0 + - - -
170A LEU* 4.0 5.9 + - - +
171A GLU* 4.0 11.1 - - - +
172A LEU* 3.7 24.0 - - + -
215A TRP* 3.7 20.6 - + + -
225A PHE* 3.9 39.3 - + + -
227A TYR* 2.5 33.6 + - - -
228A LEU* 3.5 26.2 - - + -
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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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27A GLU* 2.6 28.7 + - - -
128A ARG* 3.9 7.7 - - - +
129A SER* 3.1 22.5 + - - -
131A TYR* 1.3 74.1 - - - +
133A ALA* 1.3 65.8 + - - +
136A ILE* 2.8 39.2 + - - +
137A PHE* 2.9 19.3 + - - -
212A HIS* 5.2 2.2 - - - -
215A TRP* 3.8 13.3 - - - -
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Residues in contact with ALA 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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53A GLU* 6.2 0.2 - - - +
97A GLN* 3.7 12.5 - - - +
101A CYS* 3.7 26.0 - - - -
104A MET* 5.0 7.2 - - + -
128A ARG* 5.8 2.8 - - + +
129A SER 2.9 17.0 + - - +
130A VAL* 3.7 6.7 - - - +
132A SER* 1.3 77.5 + - - +
134A ARG* 1.3 56.0 + - - +
137A PHE* 3.6 9.4 + - - +
138A ALA* 2.8 28.6 + - - +
155A TYR* 3.7 2.8 + - - -
261A LLT 4.6 6.7 - - - +
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Residues in contact with ARG 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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130A VAL 3.1 7.3 + - - +
131A TYR 3.9 1.1 - - - +
132A SER 3.1 0.6 - - - -
133A ALA* 1.3 76.2 - - - +
135A TYR* 1.3 98.8 + - + +
136A ILE 3.4 0.4 + - - -
138A ALA* 3.5 3.5 + - - +
139A SER* 3.0 30.0 + - - -
152A TRP* 3.9 7.2 - - + -
155A TYR* 3.3 20.6 + - + +
156A GLN* 3.9 34.0 + - - +
159A HIS* 3.1 47.3 + - - +
160A ASP* 2.5 40.3 + - - -
224A ASN* 4.0 7.3 + - - +
225A PHE* 3.1 13.5 - - - -
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Residues in contact with TYR 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 TYR* 2.7 36.7 + + + +
134A ARG* 1.3 103.4 - - + +
136A ILE* 1.3 64.9 + - + +
139A SER* 3.5 16.1 + - - -
152A TRP* 5.6 4.7 - + - -
156A GLN* 5.4 3.4 - - - -
211A LYS* 3.9 5.5 + - - +
215A TRP* 6.0 4.5 - + + -
221A LEU* 4.0 35.7 - - + +
222A LYS 4.5 3.4 - - - -
223A THR* 3.5 23.8 - - + -
224A ASN* 2.6 39.7 + - + +
225A PHE* 3.2 30.9 - + - -
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Residues in contact with ILE 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 34.3 + - - +
134A ARG 4.1 0.2 - - - -
135A TYR* 1.3 78.1 - - + +
137A PHE* 1.3 73.5 + - + +
138A ALA 3.8 0.4 - - - -
140A ASN* 3.1 12.0 + - - +
208A LEU* 3.8 17.3 - - + -
211A LYS* 3.0 63.0 + - + +
212A HIS* 3.5 33.2 - - + +
215A TRP* 4.1 25.6 - - + -
221A LEU* 4.7 3.4 - - + -
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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