Contacts of the helix formed by residues 131 - 139 (chain A) in PDB entry 2YXU
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.9 35.4 - - + +
129A PRO* 3.7 20.7 - - - +
130A GLU* 1.3 74.0 + - - +
132A LEU* 1.3 61.9 + - - +
133A LEU 3.5 0.2 - - - -
134A PRO* 3.4 13.2 - - - +
135A VAL* 3.3 18.4 - - - +
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Residues in contact with LEU 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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85A THR 3.8 18.4 - - - +
86A ARG 4.1 9.0 - - - +
87A ASP 4.4 5.4 - - - -
88A LYS* 3.8 26.9 - - + +
91A LEU* 3.4 37.0 - - + -
116A LEU* 4.6 0.2 - - + -
128A VAL* 3.1 27.8 - - + -
129A PRO* 3.2 22.9 + - + +
130A GLU 2.8 1.2 + - - -
131A ASP* 1.3 80.7 - - - +
133A LEU* 1.3 67.8 + - - +
135A VAL* 2.9 11.6 + - - +
136A TYR* 2.8 34.5 + - + +
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Residues in contact with LEU 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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116A LEU* 4.0 30.3 - - + +
126A MET* 4.5 11.4 - - + +
129A PRO 4.6 0.4 + - - -
130A GLU 3.2 9.0 + - - +
132A LEU* 1.3 78.6 - - - +
134A PRO* 1.4 63.4 - - + +
136A TYR* 3.2 4.2 + - - +
137A LYS* 2.9 48.5 + - - +
156A LEU* 4.0 43.3 - - + +
157A LEU* 4.1 11.9 - - + -
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Residues in contact with PRO 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 GLU 3.4 11.2 - - - +
131A ASP* 3.4 16.4 - - - +
133A LEU* 1.4 97.4 - - + +
135A VAL* 1.3 57.9 + - + +
137A LYS* 4.7 5.6 - - + -
138A GLU* 2.8 57.1 + - - +
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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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88A LYS* 4.0 26.7 - - + +
91A LEU* 4.1 24.2 - - + -
92A ALA* 4.8 17.7 - - + +
131A ASP 3.3 22.0 - - - +
132A LEU* 2.9 7.6 + - - +
134A PRO* 1.3 78.1 - - + +
136A TYR* 1.3 56.5 + - - +
139A LYS* 2.6 52.9 + - + +
140A VAL* 3.0 9.7 + - + -
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Residues in contact with TYR 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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82A THR* 5.6 1.9 + - - -
83A GLY 3.8 18.5 + - - -
85A THR* 4.1 12.4 + - - -
91A LEU* 3.7 22.0 - - + +
112A CYS* 4.1 5.6 - - - -
113A ASP 4.0 1.6 + - - -
114A PRO* 3.8 28.7 - - + -
115A VAL 3.9 17.3 + - - -
116A LEU* 3.5 29.6 - - + -
132A LEU* 2.8 27.5 + - + -
133A LEU* 3.6 8.3 - - - +
135A VAL* 1.3 77.9 - - - +
137A LYS* 1.3 60.4 + - - +
140A VAL* 3.4 34.2 + - + -
141A VAL* 2.8 34.4 + - + +
157A LEU* 4.1 14.1 - - + -
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Residues in contact with LYS 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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133A LEU* 2.9 44.1 + - + +
134A PRO* 3.9 6.1 - - + +
136A TYR* 1.3 72.8 - - - +
138A GLU* 1.3 66.7 + - + +
141A VAL* 4.7 1.3 - - - -
142A PRO* 3.3 21.1 - - - +
156A LEU 3.4 25.0 + - - -
157A LEU* 3.7 24.2 - - + +
158A SER 5.4 0.7 - - - -
159A GLY* 5.2 6.7 - - - +
178A MET* 3.5 22.3 - - + +
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Residues in contact with GLU 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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134A PRO* 2.8 41.4 + - - +
135A VAL* 5.5 0.3 - - - -
137A LYS* 1.3 83.9 - - + +
139A LYS* 1.3 77.1 + - + +
142A PRO* 3.6 15.0 - - - +
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Residues in contact with LYS 139 (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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92A ALA* 6.5 0.2 - - - -
95A VAL* 4.1 24.8 - - + +
135A VAL* 2.6 40.1 + - + +
138A GLU* 1.3 93.1 + - + +
140A VAL* 1.3 64.8 + - - +
141A VAL 3.8 0.4 - - - -
142A PRO* 3.8 5.5 - - - +
143A LEU* 3.8 18.4 + - - +
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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