Contacts of the helix formed by residues 133 - 142 (chain A) in PDB entry 3U9J
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 VAL 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLU* 2.7 40.6 + - + +
132A GLU* 1.3 83.1 - - + +
134A PHE* 1.3 78.2 + - + +
136A PRO* 3.3 10.0 - - - +
137A MSE 3.2 32.5 + - + +
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Residues in contact with PHE 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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11A PHE* 3.9 10.5 - + + -
66A ILE* 3.6 27.8 - - + -
69A LEU* 4.3 11.1 - - + +
76A ILE* 4.6 15.3 - - + -
79A VAL* 3.7 35.7 - - + -
80A HIS* 4.6 8.5 - + + -
129A GLU* 3.4 24.0 + - - -
130A GLU* 3.1 39.9 + - + +
133A VAL* 1.3 89.1 - - + +
135A GLN* 1.3 61.0 + - - +
137A MSE 3.1 15.1 + - - +
138A LEU* 2.8 34.3 + - + +
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Residues in contact with GLN 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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4A PHE* 3.8 25.8 - - + -
8A VAL 2.9 17.3 + - - -
9A ASP* 3.7 11.0 - - - +
10A VAL* 3.2 31.7 + - - +
11A PHE* 3.7 7.9 - - + -
130A GLU 3.0 9.8 + - - +
131A GLU* 3.5 14.1 - - - +
134A PHE* 1.3 76.1 - - - +
136A PRO* 1.3 68.5 - - + +
138A LEU* 3.2 13.9 + - - +
139A MSE 2.8 55.3 + - + +
147A LEU* 4.4 4.4 - - - +
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Residues in contact with PRO 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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4A PHE* 3.9 19.1 - - + -
131A GLU 3.7 6.1 - - - +
132A GLU* 3.2 22.0 - - - +
133A VAL* 3.3 15.7 - - - +
135A GLN* 1.3 95.4 - - + +
137A MSE 1.3 62.1 + - + +
139A MSE 3.2 25.2 + - + +
140A GLU* 3.3 8.5 + - - +
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Residues in contact with MSE 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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69A LEU* 3.9 9.9 - - + -
73A SER* 3.6 21.5 - - - +
75A THR* 4.4 8.5 - - + -
76A ILE* 3.1 41.5 - - + -
133A VAL* 3.2 29.1 + - + +
134A PHE* 3.1 16.7 + - - +
136A PRO* 1.3 77.7 - - + +
138A LEU* 1.3 64.8 + - - +
140A GLU* 2.9 18.8 + - - +
141A TYR* 3.1 29.7 + - + -
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Residues in contact with LEU 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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10A VAL* 3.5 32.3 - - + -
11A PHE* 4.1 8.5 - - + -
65A ILE* 3.9 24.9 - - + +
69A LEU* 4.0 18.4 - - + -
134A PHE* 2.8 21.9 + - + +
135A GLN* 3.5 14.1 - - - +
137A MSE 1.3 72.6 - - - +
139A MSE 1.3 62.6 + - - +
142A PHE* 3.0 57.2 + - + +
147A LEU* 3.7 23.7 - - + +
150A ILE* 5.3 3.6 - - + -
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Residues in contact with MSE 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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4A PHE* 3.1 44.4 - - + -
5A PRO* 4.7 1.6 - - + -
8A VAL* 3.4 27.8 - - + -
135A GLN* 2.8 42.8 + - - +
136A PRO* 3.2 11.0 - - + +
137A MSE 3.1 0.2 - - - -
138A LEU* 1.3 76.8 - - - +
140A GLU* 1.3 59.5 + - - +
142A PHE 3.4 11.7 - - - +
144A TYR* 5.8 4.7 - - - -
147A LEU* 3.5 17.9 - - - -
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Residues in contact with GLU 140 (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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136A PRO 3.3 6.6 + - - +
137A MSE 2.9 14.1 + - - +
139A MSE 1.3 83.6 - - - +
141A TYR* 1.3 95.6 + - + +
142A PHE 3.4 2.5 + - - +
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Residues in contact with TYR 141 (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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69A LEU* 4.0 7.6 - - + -
72A ARG* 2.9 53.5 + - + -
73A SER* 3.4 43.0 + - - -
75A THR* 4.4 7.6 - - + +
137A MSE 3.1 37.0 + - + +
140A GLU* 1.3 106.3 + - + +
142A PHE* 1.3 70.0 + - + +
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Residues in contact with PHE 142 (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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68A LEU* 3.6 37.2 - - + -
69A LEU* 4.0 15.7 - - + -
72A ARG* 3.2 48.0 - - - +
138A LEU* 3.0 43.5 + - + +
139A MSE 3.4 19.2 - - - +
140A GLU 4.4 2.1 - - - +
141A TYR* 1.3 81.7 - - + +
143A THR* 1.3 65.4 + - - +
146A GLU* 3.5 14.4 - - + +
147A LEU* 3.7 17.3 - - + +
150A ILE* 4.0 19.5 - - + -
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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