Contacts of the helix formed by residues 128 - 139 (chain M) in PDB entry 3TDD
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 128 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1M THR* 6.0 0.7 - - - -
2M SER* 4.7 2.7 - - - -
127M THR* 1.3 73.4 - - - +
129M PHE* 1.3 63.5 + - - -
131M ALA* 2.9 22.1 + - - +
132M HIS* 3.6 11.7 + - - -
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Residues in contact with PHE 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242 ALA* 3.6 29.4 - - + -
252 TYR* 3.5 51.4 - + + -
1M THR* 4.7 3.6 + - - +
2M SER* 3.3 11.4 + - - +
127M THR 3.3 1.0 + - - -
128M GLY* 1.3 72.0 - - - -
130M GLY* 1.3 57.6 + - - +
132M HIS* 2.8 26.6 + - + +
133M MET* 2.9 23.2 + - + +
162M LEU* 4.1 7.6 - - + -
165M ARG 4.3 3.6 - - - -
166M ASP* 3.7 28.5 - - + +
132V LEU* 3.5 20.6 - - + -
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Residues in contact with GLY 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M SER* 2.7 24.4 + - - -
4M ILE* 4.0 1.3 - - - -
126M ALA* 3.3 12.1 - - - +
127M THR 3.1 5.9 + - - -
129M PHE* 1.3 72.6 - - - +
131M ALA* 1.3 58.6 + - - +
134M ALA* 2.7 42.3 + - - +
135M ASN 3.0 4.7 + - - -
162M LEU* 3.9 8.3 - - - -
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Residues in contact with ALA 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L SER* 4.5 14.8 + - - +
126M ALA* 3.5 20.9 - - - +
127M THR 3.7 2.6 + - - -
128M GLY 2.9 17.0 + - - +
130M GLY* 1.3 78.1 - - - +
132M HIS* 1.3 65.7 + - + +
135M ASN* 3.4 34.2 + - - +
136M PRO* 4.0 1.9 - - - +
139M ARG* 5.4 1.2 + - - -
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Residues in contact with HIS 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L TYR* 5.9 2.6 - - + +
25L SER* 3.4 25.6 + - - -
128M GLY 3.6 16.7 + - - -
129M PHE* 2.8 11.9 + - - +
131M ALA* 1.3 82.8 - - + +
133M MET* 1.3 59.0 + - - +
136M PRO* 3.1 19.9 - - - +
129V SER 5.9 2.9 - - - -
132V LEU* 3.5 31.7 - - + +
133V ALA* 3.8 14.2 + - - +
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Residues in contact with MET 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252 TYR* 4.2 8.5 - - + -
129M PHE* 2.9 17.8 + - + +
132M HIS* 1.3 81.5 - - - +
134M ALA* 1.3 64.8 + - - +
136M PRO* 3.3 7.9 - - - +
137M LEU* 3.6 8.2 - - - +
161M VAL* 3.6 27.8 - - + +
162M LEU* 3.9 17.9 - - + -
165M ARG* 3.6 37.7 - - + -
132V LEU* 3.5 34.1 - - + +
135V MET* 4.1 7.4 - - + -
136V ALA* 3.4 33.4 - - + +
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Residues in contact with ALA 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M ILE* 3.5 32.3 - - + -
126M ALA* 4.4 1.6 - - + -
130M GLY* 2.7 23.3 + - - +
133M MET* 1.3 73.0 - - - +
135M ASN* 1.3 65.0 + - - +
137M LEU* 2.9 7.2 + - - +
138M LEU* 2.9 28.3 + - + +
158M ALA* 4.2 20.0 - - + -
162M LEU* 4.4 6.4 - - + +
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Residues in contact with ASN 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L ILE 4.9 2.2 + - - -
27L ASN* 6.2 0.2 - - - +
124M THR* 2.9 35.2 + - - -
125M LEU* 3.8 3.8 + - - +
126M ALA* 3.9 17.7 + - - +
130M GLY 3.0 6.3 + - - -
131M ALA* 3.4 38.3 + - - +
134M ALA* 1.3 74.2 - - - +
136M PRO* 1.3 59.5 - - + +
138M LEU* 4.5 3.7 - - - +
139M ARG* 2.7 68.6 + - - +
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Residues in contact with PRO 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131M ALA 4.0 1.6 - - - +
132M HIS 3.1 30.1 - - - +
133M MET 3.3 10.8 - - - +
135M ASN* 1.3 94.5 - - + +
137M LEU* 1.3 61.8 + - + +
139M ARG* 3.8 2.6 + - - +
140M LYS* 3.4 25.6 + - - +
133V ALA* 3.9 23.6 - - + +
136V ALA* 5.0 1.1 - - + -
137V VAL* 5.8 0.4 - - + -
161V ALA* 4.8 5.3 - - + +
165V ASN* 3.5 41.8 - - + +
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Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133M MET 3.6 16.4 - - - +
134M ALA* 2.9 6.5 + - - +
136M PRO* 1.3 75.7 - - - +
138M LEU* 1.3 65.2 + - + +
140M LYS* 2.8 37.1 + - + +
141M VAL* 3.7 7.3 + - - +
154M ALA* 5.8 2.5 - - + +
157M ASN* 3.8 11.7 - - - +
158M ALA* 4.3 14.8 - - + -
161M VAL* 3.8 17.5 - - + -
136V ALA* 3.8 27.8 - - + +
137V VAL* 4.1 15.0 - - + +
140V SER* 3.7 22.4 - - - +
141V HIS* 5.7 1.3 - - - +
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M ILE* 4.6 2.7 - - + -
5M SER 3.8 28.5 - - - +
6M MET* 4.1 7.4 - - + +
14M VAL* 3.1 15.4 + - - +
124M THR* 3.6 18.8 - - + -
125M LEU 5.4 0.7 - - - +
126M ALA* 5.7 0.7 - - + -
134M ALA* 2.9 31.7 + - + +
135M ASN* 4.0 4.0 - - - +
137M LEU* 1.3 77.7 - - + +
139M ARG* 1.3 57.6 + - - +
141M VAL* 3.0 24.3 + - - +
154M ALA* 3.8 38.6 - - + +
155M ILE* 3.9 23.1 - - + -
158M ALA* 4.4 6.1 - - + -
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Residues in contact with ARG 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L ILE* 2.8 44.5 + - - +
27L ASN 4.2 10.9 + - - -
28L SER* 5.4 0.4 - - - +
29L ARG* 4.9 14.6 - - - +
14M VAL* 3.2 51.7 + - - +
122M SER* 5.0 6.0 + - - +
124M THR* 3.5 23.6 + - + +
135M ASN* 2.7 50.9 + - - +
136M PRO 4.1 4.3 - - - +
138M LEU* 1.3 68.3 - - - +
140M LYS* 1.3 60.8 + - - +
141M VAL 3.0 5.2 - - - -
165V ASN* 3.0 39.6 + - - +
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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