Contacts of the helix formed by residues 130 - 142 (chain Z) in PDB entry 3SDI
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 ALA 130 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2Z THR* 2.8 20.3 + - + +
129Z ALA* 1.3 71.7 - - - +
131Z ALA* 1.3 66.3 + - - +
132Z SER 3.1 3.1 - - - -
133Z LEU* 2.9 22.8 + - + +
134Z ILE* 3.2 14.9 + - + +
162Z ALA* 4.0 19.1 - - + -
166Z HIS* 4.1 13.7 - - + +
169Z VAL* 4.0 20.0 - - + -
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Residues in contact with ALA 131 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y TRP* 4.3 11.4 - - + -
2Z THR* 3.7 3.4 + - - -
98Z HIS* 5.9 2.2 - - + +
126Z ALA* 3.8 31.2 - - - +
127Z GLY* 3.9 7.4 - - - -
128Z GLY 3.1 18.0 + - - +
129Z ALA 3.3 0.6 - - - -
130Z ALA* 1.3 76.7 - - - +
132Z SER* 1.3 57.9 + - - +
134Z ILE 3.1 1.4 + - - -
135Z MET* 2.8 35.6 + - + +
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Residues in contact with SER 132 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ASP* 3.4 29.1 + - - +
133I GLN* 3.4 17.5 - - - +
25Y TRP* 3.5 31.4 - - - -
129Z ALA 4.6 6.4 + - - -
131Z ALA* 1.3 78.9 - - - +
133Z LEU* 1.3 64.6 + - - +
136Z PRO* 3.3 22.3 - - - +
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Residues in contact with LEU 133 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H ILE* 4.0 23.3 - - + -
132I ASP* 3.6 22.2 - - + +
133I GLN* 4.8 0.4 - - - +
135I PHE* 4.7 2.9 - - + -
136I GLY* 3.2 34.6 - - - +
137I MET 4.1 1.0 + - - -
139I GLU* 6.2 0.2 - - + -
140I SER* 5.4 0.5 + - - -
129Z ALA 4.9 0.7 - - - +
130Z ALA* 2.9 23.3 + - + +
132Z SER* 1.3 90.1 - - - +
134Z ILE* 1.3 66.2 + - + +
136Z PRO* 3.8 4.9 - - - +
137Z PHE* 4.4 4.5 - - - +
161Z SER 4.9 1.1 - - - +
162Z ALA* 4.6 13.5 - - - -
165Z ARG* 3.6 36.3 - - + +
166Z HIS* 4.5 6.5 - - + +
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Residues in contact with ILE 134 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z THR* 4.1 20.0 - - + -
4Z LEU* 4.2 9.9 - - + -
126Z ALA* 4.0 13.5 - - + -
130Z ALA 3.5 14.8 - - - +
131Z ALA 3.1 1.6 + - - -
133Z LEU* 1.3 83.5 - - + +
135Z MET* 1.3 66.8 + - - +
136Z PRO* 3.2 2.9 - - - -
137Z PHE* 2.9 17.7 + - + +
138Z LEU* 3.0 32.7 + - + +
158Z SER* 3.9 37.9 - - - +
159Z PHE* 5.3 2.5 - - + -
161Z SER* 6.2 0.7 - - - -
162Z ALA* 3.8 24.9 - - + +
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Residues in contact with MET 135 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I ARG* 2.7 43.7 - - - +
25Y TRP* 3.6 26.2 - - + -
124Z CYS* 4.3 17.3 - - - +
125Z ARG* 3.8 24.9 - - - +
126Z ALA* 3.6 30.6 - - + +
131Z ALA 2.8 16.7 + - - +
134Z ILE* 1.3 71.1 - - - +
136Z PRO* 1.4 70.9 - - + +
138Z LEU* 3.1 12.5 + - - +
139Z ASP* 2.9 43.9 + - - +
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Residues in contact with PRO 136 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I GLN* 3.9 24.9 - - + +
137I MET* 3.5 21.8 - - + +
161I ASN* 3.7 23.7 - - - +
165I ARG* 4.2 7.6 - - + -
25Y TRP* 4.6 0.7 - - + -
132Z SER 3.3 24.7 - - - +
133Z LEU 3.8 2.0 - - - +
134Z ILE 3.2 6.5 - - - +
135Z MET* 1.4 94.5 - - + +
137Z PHE* 1.3 61.4 + - - +
139Z ASP* 3.3 13.6 + - - +
140Z ASN* 3.1 22.0 + - - +
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Residues in contact with PHE 137 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H TYR* 3.5 38.8 - + - -
137I MET* 3.3 18.1 - - + -
140I SER* 3.5 37.2 - - - +
141I LEU* 4.5 11.0 - - + -
133Z LEU 4.4 7.8 + - - +
134Z ILE* 2.9 12.6 + - + +
136Z PRO* 1.3 79.1 - - - +
138Z LEU* 1.3 59.3 + - + +
140Z ASN* 3.0 5.7 + - - +
141Z GLN* 2.8 53.4 + - + +
154Z LEU* 4.1 17.3 - - + -
157Z ASP* 4.8 1.6 - - + -
158Z SER* 3.3 33.9 - - - -
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Residues in contact with LEU 138 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z LEU* 3.5 31.9 - - + -
6Z ILE* 4.5 6.1 - - + -
124Z CYS* 3.9 20.0 - - + -
125Z ARG 4.5 4.0 - - - +
126Z ALA* 4.3 12.8 - - + +
134Z ILE* 3.0 25.6 + - + +
135Z MET* 3.1 15.9 + - - +
137Z PHE* 1.3 81.9 - - + +
139Z ASP* 1.3 59.2 + - - +
140Z ASN 3.0 1.3 - - - -
141Z GLN* 4.3 1.6 - - + +
142Z VAL* 2.8 50.1 + - + +
143Z ASN* 3.4 1.4 + - - +
154Z LEU* 5.3 4.7 - - + -
158Z SER* 3.9 21.1 - - - +
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Residues in contact with ASP 139 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I ASN* 5.1 5.2 - - + +
164I ASP* 6.1 0.5 - - - +
165I ARG* 2.7 51.1 + - - +
124Z CYS* 5.1 2.4 - - - -
135Z MET* 2.9 27.1 + - - +
136Z PRO* 3.5 8.2 - - + +
138Z LEU* 1.3 75.4 - - - +
140Z ASN* 1.3 59.5 + - - +
143Z ASN* 3.5 13.4 - - - +
144Z LYS* 3.0 57.1 + - + +
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Residues in contact with ASN 140 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H PHE* 3.6 13.0 - - - -
137I MET* 4.2 10.5 - - + +
141I LEU* 4.3 1.0 - - - +
157I GLN* 3.1 10.1 + - - -
161I ASN* 3.1 26.9 + - - +
136Z PRO 3.1 9.6 + - - +
137Z PHE* 3.0 10.5 + - + +
138Z LEU 3.0 0.4 - - - -
139Z ASP* 1.3 81.4 - - - +
141Z GLN* 1.3 81.8 + - + +
144Z LYS* 3.0 68.9 + - - +
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Residues in contact with GLN 141 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202H LYS* 3.5 12.8 + - - -
204H TYR* 3.3 29.8 + - - +
206H PHE* 3.9 19.4 - - - -
141I LEU* 4.4 2.2 - - - +
137Z PHE* 2.8 43.2 + - + +
138Z LEU* 5.0 1.8 - - + -
140Z ASN* 1.3 95.4 + - - +
142Z VAL* 1.3 62.0 + - - +
144Z PHE* 3.6 26.8 - - - +
146Z LEU* 4.2 10.9 - - - +
154Z LEU* 3.7 21.6 - - + +
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Residues in contact with VAL 142 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Z ILE* 4.3 25.8 - - + -
7Z ALA 5.6 0.2 - - - +
123Z GLN* 4.2 17.4 - - + +
124Z CYS* 3.9 15.7 - - + -
138Z LEU* 2.8 33.3 + - + +
141Z GLN* 1.3 74.7 - - + +
143Z ASN* 1.3 71.7 + - - +
144Z PHE* 3.3 25.1 + - - +
146Z LEU* 4.2 18.3 - - + +
154Z LEU* 3.9 20.2 - - + -
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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