Contacts of the helix formed by residues 131 - 142 (chain A) in PDB entry 3MOK
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 GLY 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A SER* 3.9 11.7 - - - -
124A PRO 5.7 0.2 - - - -
127A GLN* 3.6 23.0 + - - -
128A GLY 3.1 12.4 + - - -
130A ASP* 1.3 81.1 - - - +
132A THR* 1.3 66.9 + - - -
133A VAL 3.3 2.7 - - - -
134A HIS* 3.2 6.5 + - - +
135A LYS* 3.0 20.7 + - - +
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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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121A LEU* 3.9 17.5 - - + -
123A SER* 3.2 7.8 + - - -
127A GLN* 4.9 3.9 + - - +
130A ASP 3.6 3.1 + - - -
131A GLY* 1.3 69.2 - - - -
133A VAL* 1.3 67.2 + - - +
135A LYS* 3.2 12.1 + - + +
136A VAL* 2.9 26.9 + - + +
147A ALA* 6.2 0.4 - - + -
151A GLN* 3.6 40.6 + - + +
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Residues in contact with VAL 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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73A LEU* 3.8 18.6 - - + -
85A LEU* 3.8 26.5 - - + +
86A TRP* 4.2 6.7 - - - -
87A GLY 3.5 17.7 - - - +
89A LEU* 3.9 23.6 - - + -
121A LEU* 4.0 16.2 - - + -
123A SER* 3.0 28.8 + - - +
132A THR* 1.3 76.3 - - - +
134A HIS* 1.3 62.8 + - - +
136A VAL* 3.3 4.4 + - - +
137A VAL* 3.0 27.5 + - + +
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Residues in contact with HIS 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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75A TYR* 5.3 0.4 - + - -
83A HIS 3.3 24.7 - - - -
84A THR* 3.8 2.0 - - - -
85A LEU* 3.0 45.5 + - + +
123A SER* 5.1 0.2 - - - -
128A GLY 4.1 11.7 - - - +
129A ARG* 3.4 44.5 + - + +
131A GLY* 3.2 11.7 + - - +
133A VAL* 1.3 76.2 - - - +
135A LYS* 1.3 59.6 + - + +
138A TYR* 2.8 71.8 + + + +
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Residues in contact with LYS 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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129A ARG 4.0 9.4 - - - +
130A ASP* 3.3 38.3 + - - +
131A GLY 3.0 15.4 + - - +
132A THR* 3.2 12.7 + - + +
134A HIS* 1.3 79.6 - - + +
136A VAL* 1.3 62.4 + - + +
138A TYR* 5.0 0.9 - - - -
139A GLY* 3.1 21.0 + - - -
147A ALA* 3.5 21.6 - - + +
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Residues in contact with VAL 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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89A LEU* 3.8 23.3 - - + -
92A ILE* 4.4 1.3 - - + -
121A LEU* 4.5 7.9 - - + -
132A THR* 2.9 24.8 + - + +
133A VAL 3.8 2.2 - - - +
135A LYS* 1.3 77.4 - - - +
137A VAL* 1.3 57.3 + - + +
139A GLY* 3.9 0.5 - - - -
140A LEU* 3.1 37.2 + - + +
144A ASP 4.7 0.7 - - - +
147A ALA* 3.8 16.1 - - + +
148A LEU* 4.0 42.3 + - + +
151A GLN* 4.0 18.2 - - + -
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Residues in contact with VAL 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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56A TYR* 4.0 21.5 - - + -
67A PHE* 4.1 8.8 - - + -
69A ALA* 4.2 17.9 - - + -
73A LEU* 5.2 0.4 - - + -
85A LEU* 3.8 37.7 - - + -
89A LEU* 4.0 25.8 - - + -
92A ILE* 4.5 2.7 - - + -
133A VAL* 3.0 20.3 + - + +
136A VAL* 1.3 74.2 - - + +
138A TYR* 1.3 66.4 + - - +
140A LEU* 3.2 9.0 + - - +
141A MET* 3.1 22.1 + - + +
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Residues in contact with TYR 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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75A TYR* 5.0 13.0 - + - -
85A LEU* 5.4 1.3 - - + +
129A ARG* 3.6 35.9 + - - -
134A HIS* 2.8 54.2 + + + +
135A LYS* 5.0 0.4 - - - -
137A VAL* 1.3 73.2 - - - +
139A GLY* 1.3 62.7 + - - +
141A MET* 3.1 46.4 + - + +
142A SER* 3.8 4.7 + - - -
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Residues in contact with GLY 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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135A LYS 3.1 20.6 + - - -
136A VAL 3.9 0.7 - - - -
138A TYR* 1.3 77.2 - - - +
140A LEU* 1.3 60.8 + - - +
142A SER* 3.0 14.8 + - - -
144A ASP* 2.9 39.6 + - - -
147A ALA* 5.9 0.9 - - - -
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Residues in contact with LEU 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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23A TRP* 3.6 28.3 - - + -
27A PHE* 3.7 6.8 - - - -
67A PHE* 3.4 32.1 - - + -
92A ILE* 3.9 40.4 - - + -
94A LEU* 4.5 3.4 - - + -
136A VAL* 3.1 25.2 + - + +
137A VAL* 3.2 7.2 + - - +
139A GLY* 1.3 75.2 - - - +
141A MET* 1.3 62.5 + - - +
143A GLY* 2.9 15.4 + - - +
144A ASP 3.3 12.8 + - - +
145A SER* 4.0 14.8 - - - -
148A LEU* 4.3 13.2 - - + -
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Residues in contact with MET 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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27A PHE* 3.5 14.4 - - - -
46A PHE* 6.2 0.2 - - + -
56A TYR* 3.8 28.7 - - + +
58A LEU* 3.6 29.6 - - + +
67A PHE* 3.9 1.8 - - + -
75A TYR* 5.5 5.8 - - + -
85A LEU* 3.6 31.0 - - + -
137A VAL* 3.1 15.4 + - + +
138A TYR* 3.1 45.5 + - + +
140A LEU* 1.3 77.5 - - - +
142A SER* 1.3 55.7 + - - +
143A GLY 3.4 0.2 - - - -
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Residues in contact with SER 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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27A PHE* 3.6 12.2 - - - -
28A GLY* 5.9 1.6 - - - -
138A TYR 3.8 3.5 + - - -
139A GLY* 3.0 12.9 + - - -
141A MET* 1.3 76.7 - - - +
143A GLY* 1.3 59.1 + - - +
144A ASP* 3.5 10.4 + - - +
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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