Contacts of the helix formed by residues 131 - 140 (chain A) in PDB entry 5M4G
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 GLU 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG* 3.5 19.0 + - - +
114A LYS* 4.7 2.8 + - - -
127A GLN* 3.4 19.6 - - - +
128A TYR* 3.0 28.0 + - + +
130A ASP* 1.3 94.3 - - - +
132A ILE* 1.3 65.2 + - - +
133A ALA 3.3 2.9 - - - -
134A SER* 3.1 14.0 + - - -
135A VAL* 2.9 32.6 + - + +
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Residues in contact with ILE 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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47A VAL* 4.7 2.2 - - + -
83A TYR* 3.9 38.8 - - + -
85A VAL* 4.7 4.9 - - + -
96A PHE* 3.6 31.4 - - + -
128A TYR 3.8 1.2 + - - -
129A VAL* 3.2 21.9 + - + +
130A ASP 3.5 0.6 - - - -
131A GLU* 1.3 76.0 - - - +
133A ALA* 1.3 61.2 + - + +
135A VAL* 3.8 0.3 - - - +
136A LEU* 2.9 47.5 + - + +
163A PHE* 3.7 39.5 - - + -
164A ASP 5.3 0.9 - - - +
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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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130A ASP 5.3 0.4 + - - -
131A GLU 3.3 0.6 - - - -
132A ILE* 1.3 81.9 - - - +
134A SER* 1.3 54.1 + - - +
136A LEU 3.8 0.3 - - - -
137A THR* 2.7 40.1 + - - +
163A PHE* 3.9 17.5 - - + -
164A ASP 3.5 24.5 - - - +
165A GLY* 4.6 6.7 - - - -
169A PHE* 3.8 6.8 - - + -
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Residues in contact with SER 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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131A GLU* 3.1 16.9 + - - -
133A ALA* 1.3 79.8 - - - +
135A VAL* 1.3 63.9 + - - +
137A THR* 3.3 7.0 + - - -
138A SER* 3.1 23.7 + - - -
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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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94A THR* 5.0 2.5 - - + -
96A PHE* 3.8 22.7 - - + -
125A ASP* 5.5 1.6 - - - +
127A GLN* 4.0 34.8 - - + +
131A GLU* 2.9 29.8 + - + +
132A ILE 3.8 2.7 - - - +
134A SER* 1.3 76.5 - - - +
136A LEU* 1.3 62.9 + - + +
138A SER* 2.7 25.0 + - - +
139A GLN* 3.4 28.1 + - - +
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Residues in contact with LEU 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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45A ILE* 4.1 24.7 - - + -
47A VAL* 4.3 13.5 - - + -
85A VAL* 4.3 15.3 - - + -
96A PHE* 5.0 4.7 - - + -
132A ILE* 2.9 34.4 + - + +
135A VAL* 1.3 73.2 - - - +
137A THR* 1.3 66.6 + - - +
139A GLN* 3.1 30.1 + - - +
141A PRO* 3.1 20.2 - - + +
144A LEU* 4.4 8.5 - - + -
163A PHE* 3.7 32.3 - - + -
169A PHE* 3.7 16.8 - - + -
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Residues in contact with THR 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 ALA* 2.7 26.7 + - - +
134A SER* 3.3 7.8 + - - -
136A LEU* 1.3 76.7 - - - +
138A SER* 1.3 63.5 + - - +
140A LYS* 3.1 20.6 + - - +
141A PRO* 5.0 0.4 - - - -
168A LYS* 6.2 0.2 - - - +
169A PHE* 3.5 19.0 - - - -
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Residues in contact with SER 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 SER 3.1 11.2 + - - -
135A VAL* 2.7 25.3 + - - +
137A THR* 1.3 78.0 - - - +
139A GLN* 1.3 63.4 + - - +
140A LYS* 3.3 16.8 + - - +
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Residues in contact with GLN 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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45A ILE* 3.2 30.8 - - + +
85A VAL* 5.0 4.5 - - - +
87A ASP* 5.6 2.4 - - - +
92A LYS* 4.1 23.7 - - - +
94A THR* 4.5 9.5 + - - -
125A ASP* 5.9 0.4 + - - -
135A VAL* 3.5 34.6 - - - +
136A LEU* 3.1 17.5 + - - +
138A SER* 1.3 79.3 - - - +
140A LYS* 1.3 71.7 + - - +
141A PRO* 3.4 1.4 - - - +
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Residues in contact with LYS 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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43A GLY* 4.9 1.6 - - - +
137A THR 3.1 14.3 + - - +
138A SER* 4.0 13.2 + - - +
139A GLN* 1.3 81.3 - - - +
141A PRO* 1.3 73.5 - - - +
142A SER 3.8 0.7 + - - -
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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