Contacts of the helix formed by residues 130 - 142 (chain H) 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 130 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1H THR 3.0 8.5 + - - -
2H THR* 3.1 27.7 - - - +
129H SER* 1.3 76.2 - - - +
131H SER* 1.3 64.1 + - - +
132H LEU 3.1 2.9 - - - -
133H ALA* 2.8 18.9 + - - +
134H ALA* 2.9 13.7 + - - +
162H GLY* 4.3 3.4 - - - -
166H ASP* 3.4 15.8 + - - -
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Residues in contact with SER 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H SER* 2.9 39.5 + - - -
127H LEU* 3.6 11.5 + - - +
128H GLY 2.6 26.9 + - - -
129H SER 3.1 1.0 - - - -
130H GLY* 1.3 75.5 - - - +
132H LEU* 1.3 69.6 + - - +
134H ALA* 4.7 0.2 - - - -
135H MET* 2.9 26.3 + - - +
25N TYR* 4.6 8.2 + - - -
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Residues in contact with LEU 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1291 PHE* 3.5 27.6 - - + -
1321 HIS* 3.5 38.8 - - + +
1331 MET* 3.6 17.0 - - + +
129H SER 4.6 3.7 + - - +
130H GLY 3.0 1.0 + - - -
131H SER* 1.3 86.7 - - - +
133H ALA* 1.3 66.7 + - - +
135H MET* 4.4 3.8 - - - +
136H ALA* 3.0 24.1 + - - +
25N TYR* 3.5 42.0 - - + -
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Residues in contact with ALA 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1321 HIS 3.9 10.6 + - - +
1361 PRO* 4.0 18.9 - - + +
129H SER 5.4 0.4 + - - -
130H GLY* 2.8 14.6 + - - +
132H LEU* 1.3 76.5 - - - +
134H ALA* 1.3 62.8 + - - +
136H ALA* 3.4 9.9 + - - +
137H VAL* 3.4 7.4 + - - +
161H ALA* 3.3 42.3 - - + +
162H GLY* 3.8 4.9 - - - +
165H ASN* 4.4 4.5 - - + -
166H ASP* 5.3 2.5 - - + -
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Residues in contact with ALA 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H THR* 4.0 7.6 - - + -
4H VAL* 3.7 26.5 - - + -
126H SER* 4.0 5.6 - - - -
130H GLY 2.9 13.6 + - - +
131H SER 3.8 3.4 - - - +
133H ALA* 1.3 75.3 - - - +
135H MET* 1.3 66.0 + - - +
137H VAL* 3.0 7.3 + - - +
138H LEU* 3.0 24.3 + - - +
158H ALA* 3.4 26.9 - - + +
161H ALA* 4.0 0.4 - - - +
162H GLY 4.7 0.2 - - - +
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Residues in contact with MET 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331 MET* 4.1 2.9 - - + -
1651 ARG* 3.6 47.6 - - + +
124H TYR* 3.8 30.7 - - + +
125H LEU* 4.5 2.5 - - + -
126H SER* 3.7 26.2 + - - +
131H SER 2.9 19.8 + - - +
132H LEU* 4.0 3.4 - - - +
134H ALA* 1.3 75.9 - - - +
136H ALA* 1.3 58.6 + - - +
138H LEU* 4.2 7.0 - - + -
139H GLU* 2.8 40.7 + - + +
25N TYR* 3.5 19.7 - - - +
27N ALA 5.3 1.3 - - - +
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Residues in contact with ALA 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331 MET* 3.3 39.0 - - + +
1361 PRO* 5.0 1.6 - - + -
1371 LEU* 3.8 16.8 - - + -
1611 VAL* 3.9 7.6 - - + +
132H LEU 3.0 14.6 + - - +
133H ALA* 3.5 11.2 - - - +
134H ALA 3.2 0.4 - - - -
135H MET* 1.3 75.3 - - - +
137H VAL* 1.3 61.1 + - - +
139H GLU* 3.5 2.1 + - - +
140H SER* 2.9 29.8 + - - -
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Residues in contact with VAL 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1361 PRO* 5.8 1.1 - - + -
1371 LEU* 4.2 14.6 - - + -
1401 LYS* 4.4 18.8 - - + +
133H ALA 3.4 1.8 + - - +
134H ALA 3.0 8.0 + - - +
136H ALA* 1.3 76.5 - - - +
138H LEU* 1.3 66.3 + - - +
140H SER* 3.0 5.7 + - - -
141H HIS* 2.9 39.9 + - + +
154H LEU* 4.2 8.1 - - + -
157H ASP* 4.1 14.1 - - + +
158H ALA* 3.9 22.2 - - - +
161H ALA* 3.6 29.2 - - + -
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H VAL* 4.4 7.6 - - + -
6H VAL* 3.9 19.5 - - + -
124H TYR* 3.5 30.3 - - + -
125H LEU 4.0 22.4 - - - +
126H SER* 4.2 10.5 - - - -
134H ALA 3.0 21.4 + - - +
135H MET* 3.8 12.8 - - - +
137H VAL* 1.3 75.8 - - - +
139H GLU* 1.3 62.6 + - - +
142H TRP* 2.9 30.9 + - - +
154H LEU* 3.9 29.4 - - + +
158H ALA* 4.0 15.0 - - + -
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Residues in contact with GLU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1571 ASN* 5.4 1.2 + - - -
1601 ARG* 5.6 1.9 + - - -
1611 VAL* 4.2 17.6 - - + +
1641 TYR* 3.7 23.7 - - + +
1651 ARG* 2.5 38.8 + - + +
1961 LYS* 5.4 7.3 + - - +
124H TYR* 2.8 25.2 + - - -
135H MET* 2.8 36.3 + - + +
136H ALA 3.9 3.8 - - - +
138H LEU* 1.3 73.2 - - - +
140H SER* 1.3 59.2 + - - +
142H TRP 4.8 1.8 + - - +
29N ARG* 2.7 27.0 + - - -
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Residues in contact with SER 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 LEU* 3.7 9.1 - - - +
1571 ASN* 2.9 33.8 + - - +
1611 VAL* 3.5 9.5 - - - +
1961 LYS* 5.4 5.0 + - - -
136H ALA 2.9 20.0 + - - -
137H VAL* 3.0 7.4 + - - -
139H GLU* 1.3 80.1 - - - +
141H HIS* 1.3 81.8 + - - +
142H TRP 5.3 0.9 - - - -
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Residues in contact with HIS 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 LEU* 5.6 1.6 - - - +
1401 LYS* 4.4 18.8 + - - -
137H VAL* 2.9 33.7 + - + -
140H SER* 1.3 100.8 + - - +
142H TRP* 1.3 69.2 + - - +
143H LYS* 3.6 9.0 + - - +
146H LEU* 4.6 3.6 - - - +
154H LEU* 3.7 22.6 - - + +
157H ASP* 5.2 7.6 - - - -
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Residues in contact with TRP 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1961 LYS* 3.4 31.6 + - + +
1991 PHE* 4.0 26.7 - + + -
6H VAL* 4.1 2.5 - - + -
7H LYS* 4.0 11.6 + - + -
123H TYR* 3.3 48.6 + + + +
124H TYR* 3.7 38.8 - + + -
138H LEU* 2.9 20.0 + - - +
139H GLU 4.8 1.8 - - - +
140H SER 5.3 0.7 - - - -
141H HIS* 1.3 80.3 - - - +
143H LYS* 1.3 85.4 + - - +
144H GLN* 3.8 33.2 - - + -
145H ASP 5.3 0.4 - - - -
146H LEU* 3.6 22.6 - - + +
154H LEU* 3.7 16.6 - - + +
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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