Contacts of the helix formed by residues 128 - 139 (chain A) in PDB entry 3BWC
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 2.6 32.4 + - - +
46A LYS 5.3 0.2 + - - -
47A PHE* 4.0 13.4 - - + +
48A GLN* 3.2 22.0 + - - +
126A ASP* 2.8 12.1 + - - +
127A ILE* 1.3 78.2 - - + +
129A GLY* 1.3 62.8 + - - +
130A GLU* 3.0 25.1 + - - +
131A VAL* 3.4 23.4 + - + +
132A MSE 3.6 8.2 - - - +
155A VAL* 4.5 0.4 - - - -
501A SAM 3.4 17.5 - - - +
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Residues in contact with GLY 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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47A PHE* 5.2 1.6 - - - -
127A ILE 3.8 0.4 + - - -
128A ASP* 1.3 73.4 + - - +
130A GLU* 1.3 59.4 + - - +
131A VAL 3.3 0.2 - - - -
132A MSE 3.5 8.8 + - - +
133A GLU* 3.2 30.3 + - - +
155A VAL* 3.7 35.2 - - - +
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Residues in contact with GLU 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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41A TYR* 3.0 25.4 + - - +
44A PRO 5.3 0.5 - - - +
45A THR* 3.6 30.4 - - + +
46A LYS* 4.6 12.3 + - - +
50A LEU* 4.1 4.7 - - + -
128A ASP* 3.0 11.7 + - - +
129A GLY* 1.3 74.7 - - - +
131A VAL* 1.3 60.2 + - - +
133A GLU* 4.1 9.0 - - + -
134A GLN* 3.0 37.4 + - + +
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Residues in contact with VAL 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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48A GLN* 3.8 7.4 - - - +
50A LEU* 4.1 12.3 - - + -
65A MSE 4.2 12.8 - - - +
67A LEU* 4.1 16.6 - - + -
105A GLY* 4.3 4.3 - - - -
106A ASP* 4.2 14.1 - - + +
126A ASP* 4.6 0.2 - - - +
128A ASP* 3.4 33.2 + - + +
129A GLY 3.3 0.2 - - - -
130A GLU* 1.3 78.7 - - - +
132A MSE 1.3 53.1 + - - +
134A GLN* 3.9 1.6 - - - +
135A SER* 2.6 43.7 + - - +
501A SAM 3.4 31.0 - - + +
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Residues in contact with MSE 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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105A GLY* 2.9 33.9 - - - +
126A ASP* 3.7 24.0 - - - -
128A ASP 3.6 20.9 - - - +
129A GLY* 3.5 9.3 + - - +
130A GLU 3.3 0.2 - - - -
131A VAL* 1.3 74.0 - - - +
133A GLU* 1.3 61.9 + - - +
135A SER* 3.6 1.8 - - - -
136A LYS* 2.9 46.4 + - - +
146A LEU* 4.1 13.1 - - + +
153A VAL* 3.3 31.4 - - + -
154A ARG 4.6 2.2 - - - +
155A VAL* 3.5 26.9 - - + -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLY 3.2 20.2 + - - +
130A GLU* 3.8 11.4 - - + +
131A VAL 3.4 0.2 - - - -
132A MSE 1.3 77.8 - - - +
134A GLN* 1.3 69.9 + - - +
136A LYS* 2.7 37.3 + - - +
137A GLN* 3.3 20.8 + - - +
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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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41A TYR* 3.2 43.4 + - + -
50A LEU* 3.5 18.6 - - + -
52A ILE* 3.4 20.2 - - + +
65A MSE 4.6 0.2 - - + -
130A GLU* 3.0 22.8 + - + +
131A VAL 4.1 1.3 - - - +
133A GLU* 1.3 80.6 - - - +
135A SER* 1.3 59.8 - - - +
137A GLN* 3.8 12.3 + - - +
138A HIS* 3.0 59.2 + - - +
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Residues in contact with SER 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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65A MSE 3.4 19.0 - - - +
106A ASP* 3.4 38.2 - - - +
131A VAL* 2.6 23.9 + - - +
132A MSE 3.6 7.0 - - - -
133A GLU 3.3 0.2 - - - -
134A GLN* 1.3 75.0 - - - +
136A LYS* 1.3 58.3 + - - +
139A PHE* 2.8 44.1 + - - +
143A SER* 3.4 4.7 - - - -
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Residues in contact with LYS 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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129A GLY 5.7 0.2 + - - -
132A MSE 2.9 31.2 + - - +
133A GLU* 2.7 39.4 + - - +
135A SER* 1.3 78.9 - - - +
137A GLN* 1.3 62.0 + - - +
140A PRO* 3.9 17.5 - - - +
143A SER* 3.2 19.7 + - - +
146A LEU* 4.3 18.4 - - + -
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU 3.3 11.9 + - - +
134A GLN* 3.9 14.5 + - - +
135A SER 3.2 0.6 - - - -
136A LYS* 1.3 81.8 - - - +
138A HIS* 1.3 93.0 + - + +
140A PRO* 4.2 7.4 - - - +
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Residues in contact with HIS 138 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.4 51.7 + - + +
52A ILE* 4.0 27.8 - - + -
63A THR* 3.8 14.0 + - + +
75A ASP* 5.0 0.5 - - - +
134A GLN* 3.0 46.5 + - - +
137A GLN* 1.3 104.0 + - + +
139A PHE* 1.3 71.7 + - + +
140A PRO* 3.4 8.4 - - - +
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Residues in contact with PHE 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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52A ILE* 4.2 7.6 - - + -
63A THR* 3.4 40.8 - - + -
65A MSE 3.5 54.7 - - + -
73A VAL* 4.0 15.7 - - + -
75A ASP* 3.3 27.8 - - - -
106A ASP* 6.0 2.2 - - + -
135A SER* 2.8 24.1 + - - +
138A HIS* 1.3 77.2 - - + +
140A PRO* 1.3 58.4 - - - +
141A GLN 3.3 3.4 - - - -
142A ILE* 3.2 30.2 + - + -
143A SER* 2.7 28.1 + - - -
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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