Contacts of the helix formed by residues 130 - 142 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2W ILE* 3.5 18.0 - - + +
128W GLY 3.2 0.8 - - - -
129W THR* 1.3 78.0 + - - +
131W SER* 1.3 62.4 + - - +
132W ASP 3.3 3.1 - - - -
133W GLN* 3.0 14.6 + - + +
134W LEU* 2.9 25.3 + - - +
162W ALA* 3.8 19.7 - - + +
166W ASP* 3.2 27.5 + - + +
169W SER* 4.5 0.7 - - - +
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Residues in contact with SER 131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22V GLN* 6.2 0.9 - - - -
126W VAL* 3.8 15.2 - - - +
127W SER* 4.5 2.2 - - - -
128W GLY 2.8 18.6 + - - -
129W THR 3.4 2.1 + - - -
130W ALA* 1.3 76.1 - - - +
132W ASP* 1.3 58.7 + - - +
134W LEU* 3.1 10.9 + - - +
135W PHE* 2.7 46.2 + - - -
201W MG 2.5 28.9 - - - -
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Residues in contact with ASP 132 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L SER* 3.2 29.6 + - - +
133L LEU* 3.8 13.2 - - + +
25V ILE* 3.6 29.1 - - - +
130W ALA 3.3 0.4 - - - -
131W SER* 1.3 78.8 + - - +
133W GLN* 1.3 71.9 + - - +
135W PHE* 3.2 10.9 + - - +
136W GLY* 3.0 17.8 + - - -
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Residues in contact with GLN 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ASN 5.4 0.4 + - - -
25K TRP* 3.6 18.8 - - + +
132L SER* 3.2 22.4 - - - +
133L LEU 4.4 1.2 - - - +
136L PRO* 3.7 14.7 - - + +
129W THR 4.5 2.5 + - - +
130W ALA* 3.0 21.7 + - - +
132W ASP* 1.3 81.7 - - - +
134W LEU* 1.3 57.2 + - - +
136W GLY* 3.0 3.6 + - - -
137W MET* 2.9 31.5 + - - +
162W ALA* 3.7 24.0 - - + +
165W ARG* 3.2 36.8 + - + -
166W ASP* 4.1 10.9 + - - +
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Residues in contact with LEU 134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2W ILE* 3.7 35.9 - - + -
3W VAL 4.0 10.8 - - - +
4W VAL* 3.9 28.7 - - + -
126W VAL* 3.7 16.8 - - + -
127W SER 3.8 12.8 - - - +
130W ALA 2.9 11.0 + - - +
131W SER* 3.4 7.0 - - - +
133W GLN* 1.3 74.2 - - - +
135W PHE* 1.3 64.9 + - - +
137W MET* 3.9 1.5 - - - +
138W CYS* 3.0 30.8 + - - -
158W ALA* 4.0 13.0 - - + +
159W LEU* 4.1 7.4 - - + -
162W ALA* 3.6 23.8 - - + -
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Residues in contact with PHE 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L LEU* 4.8 8.3 - - + -
165L ARG* 3.2 41.1 - - - +
22V GLN* 4.6 14.1 - - - -
25V ILE* 3.6 30.5 - - + -
26V VAL 3.8 1.6 - - - -
27V ALA* 3.8 25.6 - - + -
120W ASP* 5.5 2.7 - - - -
124W PHE* 4.1 15.4 - + - -
125W ILE* 6.1 0.2 - - - -
126W VAL* 3.5 26.4 - - + +
131W SER* 2.7 33.7 + - - -
132W ASP* 3.2 10.1 + - - +
134W LEU* 1.3 73.1 - - - +
136W GLY* 1.3 61.9 + - - +
138W CYS* 4.3 1.5 - - - +
139W GLU* 3.1 27.7 + - - +
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Residues in contact with GLY 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L LEU* 3.2 41.3 - - - +
137L PHE* 5.4 0.4 - - - -
161L SER* 4.9 2.4 - - - -
132W ASP 3.0 6.5 + - - -
133W GLN 3.0 5.5 + - - -
135W PHE* 1.3 75.8 - - - +
137W MET* 1.3 63.6 + - - +
139W GLU* 4.2 1.9 - - - +
140W SER* 2.9 30.0 + - - -
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Residues in contact with MET 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133L LEU 4.2 0.4 + - - -
136L PRO* 3.5 10.5 - - + +
137L PHE* 3.3 34.5 - - + -
140L ASN* 4.1 13.0 - - + +
133W GLN 2.9 17.7 + - - +
134W LEU* 3.9 3.8 - - - +
136W GLY* 1.3 74.6 - - - +
138W CYS* 1.3 52.5 + - - +
140W SER* 3.2 3.3 + - - -
141W LEU* 2.7 71.7 + - + +
157W GLN 3.8 13.0 - - - +
158W ALA* 3.5 31.2 - - + +
161W ASN* 3.8 12.1 - - + +
162W ALA* 4.0 9.9 - - + +
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Residues in contact with CYS 138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4W VAL* 3.8 20.4 - - - -
6W MET* 3.7 28.3 - - + -
124W PHE* 3.4 33.2 - - + -
126W VAL* 4.0 8.3 - - - -
134W LEU* 3.0 25.7 + - - +
137W MET* 1.3 70.7 - - - +
139W GLU* 1.3 67.9 + - - +
141W LEU* 4.4 1.1 - - - +
142W TYR* 2.8 31.8 + - + +
158W ALA* 4.2 8.1 - - - -
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Residues in contact with GLU 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161L SER* 3.7 11.0 - - - +
164L GLU* 3.5 15.7 - - + +
165L ARG* 2.6 47.9 + - + -
29V LYS* 2.6 26.2 + - - -
197V ARG* 2.8 51.4 + - - +
200V LYS* 3.5 8.7 + - - -
124W PHE* 3.4 11.7 - - + -
135W PHE 3.1 20.2 + - - +
136W GLY* 4.2 2.7 - - - +
138W CYS* 1.3 77.3 - - - +
140W SER* 1.3 59.5 + - - +
142W TYR* 4.5 2.0 + - - +
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Residues in contact with SER 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L PHE* 3.6 43.3 - - - +
157L ASP* 5.1 0.4 + - - -
158L SER* 5.2 0.2 - - - -
161L SER* 3.1 22.9 + - - -
200V LYS* 3.0 27.3 + - - +
204V TYR* 3.6 9.6 - - - -
136W GLY 2.9 18.7 + - - -
137W MET 3.2 3.3 + - - -
138W CYS 3.0 0.6 - - - -
139W GLU* 1.3 77.6 - - - +
141W LEU* 1.3 63.2 + - - +
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Residues in contact with LEU 141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L PHE* 4.2 17.9 - - + -
140L ASN* 4.2 6.7 - - - +
141L GLN* 4.3 1.6 - - - +
200V LYS* 5.5 0.2 - - - -
204V TYR* 3.9 31.0 + - + +
206V PHE* 3.9 22.4 - - + -
137W MET* 2.7 45.3 + - + +
138W CYS* 4.5 1.8 - - - +
140W SER* 1.3 74.4 - - - +
142W TYR* 1.3 64.1 + - - +
143W GLU* 3.7 6.1 + - - +
154W THR* 3.8 28.7 + - + +
157W GLN* 4.0 11.0 - - + -
158W ALA* 3.7 24.9 - - + +
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Residues in contact with TYR 142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200V LYS* 3.4 21.3 + - - -
6W MET* 3.6 28.5 - - + -
7W THR* 3.0 39.7 + - - -
122W LYS* 4.2 6.0 + - - -
123W ASP* 3.4 42.5 + - + -
124W PHE* 4.0 12.3 - + + -
138W CYS* 2.8 23.0 + - - +
139W GLU 4.7 1.6 - - - +
140W SER 3.5 0.6 - - - -
141W LEU* 1.3 78.6 - - - +
143W GLU* 1.3 95.7 + - - +
144W PRO* 3.7 14.8 - - + +
145W ASN 4.9 0.9 + - - -
146W LEU* 5.0 2.9 - - + -
151W LEU* 4.9 2.5 - - + -
154W THR* 4.4 6.3 - - - +
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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