Contacts of the helix formed by residues 130 - 142 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2L THR* 2.9 25.8 + - + +
129L ALA* 1.3 71.5 - - - +
131L ALA* 1.3 64.2 + - - +
132L SER 3.2 2.5 - - - -
133L LEU* 3.2 18.4 + - + +
134L ILE* 3.0 23.5 + - + +
162L ALA* 3.9 21.3 - - + -
166L HIS* 4.0 7.6 - - + +
169L VAL* 3.9 16.8 - - + -
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Residues in contact with ALA 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TRP* 4.4 9.0 - - + -
2L THR* 4.4 0.4 - - - +
126L ALA* 3.6 32.1 - - - +
127L GLY* 3.8 10.5 - - - -
128L GLY 3.2 18.2 + - - +
129L ALA 3.2 3.2 - - - -
130L ALA* 1.3 79.3 - - - +
132L SER* 1.3 59.0 + - - +
135L MET* 2.9 34.7 + - - +
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Residues in contact with SER 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TRP* 3.7 28.5 - - - -
129L ALA 4.5 6.2 + - - -
131L ALA* 1.3 79.3 - - - +
133L LEU* 1.3 67.1 + - - +
136L PRO* 3.3 9.8 - - - +
132W ASP* 3.2 32.6 + - - +
133W GLN* 3.2 28.0 - - - +
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Residues in contact with LEU 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L ALA 4.8 0.7 - - - +
130L ALA* 3.2 24.4 + - + +
131L ALA 3.2 0.4 - - - -
132L SER* 1.3 93.6 + - - +
134L ILE* 1.3 65.1 + - + +
136L PRO* 3.5 8.4 - - - +
137L PHE* 4.5 4.2 + - - +
161L SER 5.0 0.9 - - - +
162L ALA* 4.5 14.6 - - - +
165L ARG* 3.6 38.4 - - + +
166L HIS* 4.0 7.0 - - + +
25V ILE* 3.9 23.3 - - + -
132W ASP* 3.8 14.6 - - + +
135W PHE* 4.8 3.4 - - + -
136W GLY* 3.2 38.4 - - - +
137W MET 4.2 0.5 + - - -
140W SER* 5.5 0.2 + - - -
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Residues in contact with ILE 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 4.1 15.0 - - + -
4L LEU* 4.1 9.2 - - + -
126L ALA* 4.0 11.2 - - + -
130L ALA* 3.0 20.2 + - + +
133L LEU* 1.3 80.3 - - + +
135L MET* 1.3 65.0 + - - +
136L PRO* 3.4 0.9 - - - -
137L PHE* 3.2 9.3 + - + +
138L LEU* 3.1 35.0 + - + +
158L SER* 3.7 43.5 - - - +
159L PHE* 5.0 5.8 - - + +
161L SER* 6.0 0.9 - - - -
162L ALA* 3.5 28.7 - - + +
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Residues in contact with MET 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TRP* 3.7 22.7 - - + -
122L GLU* 6.1 0.2 - - - -
124L CYS* 4.0 19.1 - - - +
125L ARG* 3.8 23.1 - - - +
126L ALA* 3.4 38.0 - - + +
131L ALA 2.9 23.5 + - - +
134L ILE* 1.3 72.8 - - - +
136L PRO* 1.4 61.2 - - + +
138L LEU* 3.1 13.3 + - - +
139L ASP* 2.9 35.5 + - - +
165W ARG* 2.7 41.7 - - - +
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Residues in contact with PRO 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K TRP* 4.7 0.2 - - + -
132L SER 3.3 25.1 - - - +
133L LEU 3.5 5.2 - - - +
134L ILE 3.4 4.0 - - - -
135L MET* 1.4 93.6 - - + +
137L PHE* 1.3 60.3 + - - +
139L ASP* 3.3 16.1 + - - +
140L ASN* 3.2 22.2 + - - +
133W GLN* 3.7 24.0 - - + -
137W MET* 3.5 19.3 - - + +
161W ASN* 3.5 24.4 - - - +
162W ALA 4.4 0.4 - - - +
165W ARG* 3.9 8.5 - - + -
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Residues in contact with PHE 137 (chain L).
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 4.5 4.9 - - - +
134L ILE* 3.2 12.7 + - + +
136L PRO* 1.3 80.1 - - - +
138L LEU* 1.3 62.7 + - + +
140L ASN* 3.1 3.6 + - - +
141L GLN* 2.8 48.8 + - + +
154L LEU* 3.9 18.4 - - + -
157L ASP* 4.8 1.3 - - + -
158L SER* 3.2 33.0 - - - -
204V TYR* 3.3 40.6 - + - -
136W GLY 5.1 0.7 - - - +
137W MET* 3.3 16.6 - - + -
140W SER* 3.6 36.6 - - - +
141W LEU* 4.2 13.0 - - + -
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L LEU* 3.2 34.8 - - + -
6L ILE* 4.7 6.3 - - + -
124L CYS* 4.0 19.8 - - + -
125L ARG 4.4 8.5 - - - -
126L ALA* 4.2 11.2 - - + -
134L ILE* 3.1 22.7 + - + +
135L MET* 3.1 13.2 + - - +
137L PHE* 1.3 79.1 - - + +
139L ASP* 1.3 66.7 + - - +
140L ASN 3.0 1.6 - - - -
141L GLN* 5.0 0.2 - - - -
142L VAL* 2.8 47.5 + - + +
143L ASN 3.5 1.0 + - - -
154L LEU* 5.2 6.1 - - + +
158L SER* 3.8 22.2 - - - +
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Residues in contact with ASP 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L CYS* 5.5 2.0 - - - -
135L MET* 2.9 19.7 + - - +
136L PRO* 3.3 9.6 + - - +
138L LEU* 1.3 75.4 - - - +
140L ASN* 1.3 58.8 + - - +
143L ASN* 3.5 12.8 + - - +
144L LYS* 3.1 51.5 + - + +
161W ASN* 4.8 6.4 - - + +
164W ASP* 5.8 1.9 - - - +
165W ARG* 2.8 54.3 + - - +
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Residues in contact with ASN 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136L PRO 3.2 11.3 + - - +
137L PHE 3.1 8.4 + - - +
138L LEU 3.0 0.6 - - - -
139L ASP* 1.3 79.2 - - - +
141L GLN* 1.3 79.1 + - + +
144L LYS* 2.9 72.1 + - - +
206V PHE* 3.5 14.2 - - - -
137W MET* 4.1 12.8 - - + +
141W LEU* 4.2 1.0 - - - +
157W GLN* 3.0 17.6 + - - -
161W ASN* 3.2 20.6 + - - +
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Residues in contact with GLN 141 (chain L).
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* 2.8 45.3 + - + +
138L LEU* 4.8 0.7 - - - +
140L ASN* 1.3 97.8 + - - +
142L VAL* 1.3 61.4 + - + +
144L PHE* 3.5 26.2 - - - +
146L LEU* 4.5 4.3 - - - +
150L GLU* 5.7 0.7 - - - +
154L LEU* 3.4 28.4 - - + +
202V LYS* 3.6 14.9 + - - -
204V TYR* 3.5 26.5 + - - +
206V PHE* 4.0 18.4 - - - -
141W LEU* 4.3 2.2 - - - +
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Residues in contact with VAL 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ILE* 4.3 22.4 - - + -
7L ALA 5.6 0.2 - - - +
123L GLN* 4.2 14.5 - - + +
124L CYS* 3.9 14.6 - - - -
138L LEU* 2.8 43.6 + - + +
141L GLN* 1.3 77.2 - - + +
143L ASN* 1.3 70.3 + - - +
144L PHE* 3.4 25.7 + - - +
146L LEU* 4.3 13.4 - - + +
154L LEU* 4.1 17.9 - - + -
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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