Contacts of the helix formed by residues 123 - 132 (chain L) in PDB entry 5DST
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 123 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120L SER* 3.1 14.7 + - - -
121L GLY 3.0 7.3 - - - -
122L THR* 1.3 78.8 - - - +
124L ILE* 1.3 64.8 + - - +
125L LEU 3.2 3.2 + - - -
126L SER* 3.3 12.2 + - - -
127L MET* 2.9 30.6 + - - +
149L SER* 4.2 7.0 - - - -
153L ILE* 4.8 8.3 - - - -
164L ILE* 5.4 0.4 - - - -
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Residues in contact with ILE 124 (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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242K VAL* 4.0 15.7 - - + +
243K TYR* 4.5 1.3 - - + -
245K PHE* 3.8 20.2 - - + -
247K MET* 4.2 15.3 - - + -
90L LEU* 3.8 24.2 - - + -
95L ARG* 4.7 2.2 - - - +
96L THR* 4.5 3.1 - - + -
120L SER 4.2 0.2 + - - -
122L THR* 3.4 6.8 - - - +
123L GLY* 1.3 76.9 - - - +
125L LEU* 1.3 66.1 + - + +
127L MET* 3.3 7.6 + - + +
128L PHE* 3.0 58.7 + - + -
401L SAH 3.6 33.0 - - - +
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Residues in contact with LEU 125 (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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95L ARG* 5.5 2.9 - - - +
96L THR* 5.6 1.3 - - + -
99L TYR* 3.8 44.0 - - + -
103L MET* 3.9 2.5 - - + +
117L ASP* 3.2 20.1 + - - +
120L SER 4.8 0.8 + - - -
123L GLY 3.2 0.6 - - - -
124L ILE* 1.3 80.2 - - + +
126L SER* 1.3 67.6 + - - +
128L PHE* 3.1 30.2 + - + +
129L ALA 3.1 9.7 + - - -
183L ILE* 3.6 16.6 - - + +
184L SER* 4.3 4.0 - - - +
185L GLU* 3.9 21.8 - - + +
401L SAH 3.4 34.5 - - - +
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Residues in contact with SER 126 (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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117L ASP* 2.9 35.4 + - - +
120L SER* 4.3 4.5 - - - -
123L GLY* 3.6 10.1 - - - -
125L LEU* 1.3 76.0 - - - +
127L MET* 1.3 61.8 + - - +
129L ALA* 3.3 3.3 + - - +
130L ALA* 3.1 18.4 + - - +
137L VAL* 3.6 23.7 - - - +
139L GLY* 4.2 9.0 - - - -
153L ILE* 5.3 0.2 - - - -
162L ILE* 3.6 24.6 - - - +
164L ILE* 4.7 1.3 - - - +
183L ILE* 4.4 3.6 - - - -
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Residues in contact with MET 127 (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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245K PHE* 3.6 52.0 - - + -
247K MET* 4.3 8.5 - - + -
122L THR 5.0 0.2 - - - +
123L GLY 2.9 23.6 + - - +
124L ILE* 3.7 13.5 - - - +
125L LEU 3.2 0.2 - - - -
126L SER* 1.3 73.3 - - - +
128L PHE* 1.3 65.0 + - - +
130L ALA* 3.6 1.7 + - - +
131L LYS* 3.1 27.2 + - - +
152L ILE* 3.9 21.1 - - + -
153L ILE* 4.1 14.6 - - + -
156L ASN* 3.8 15.0 - - - -
158L LEU* 3.9 10.7 - - + +
162L ILE* 3.7 20.9 - - + -
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Residues in contact with PHE 128 (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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243K TYR* 4.0 9.4 - + + -
245K PHE* 3.7 20.2 - + - -
96L THR* 3.8 27.4 - - + -
99L TYR 4.3 1.8 - - - -
100L ARG* 3.5 54.7 - - + -
103L MET* 3.8 13.5 - - + -
104L TYR* 3.3 26.2 - - + -
124L ILE* 3.0 39.9 + - + -
125L LEU* 3.1 25.5 + - + +
127L MET* 1.3 76.5 - - - +
129L ALA* 1.3 64.3 + - - +
131L LYS 3.2 2.3 + - - -
132L ALA* 2.9 20.4 + - - +
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Residues in contact with ALA 129 (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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103L MET* 3.6 16.4 - - - -
110L PHE* 4.4 7.6 - - + +
115L VAL* 4.2 13.5 - - + -
125L LEU 3.1 11.2 + - - +
126L SER* 3.6 7.9 - - - +
128L PHE* 1.3 76.9 - - - +
130L ALA* 1.3 63.8 + - - +
132L ALA* 2.9 17.9 + - - +
133L GLY 3.2 7.8 + - - -
134L ALA* 3.3 10.8 + - - +
137L VAL* 4.0 13.9 - - + -
183L ILE* 4.1 12.6 - - + -
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Residues in contact with ALA 130 (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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126L SER 3.1 16.3 + - - +
127L MET 3.8 4.3 - - - +
129L ALA* 1.3 75.8 - - - +
131L LYS* 1.3 56.8 + - - +
133L GLY* 3.1 19.4 + - - -
134L ALA 3.7 6.9 + - - +
137L VAL* 3.9 7.3 - - + +
158L LEU* 4.4 16.8 - - + -
161L ILE* 3.8 30.8 - - + +
162L ILE* 3.9 15.5 - - + -
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Residues in contact with LYS 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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245K PHE* 3.9 19.1 - - + -
104L TYR* 3.5 30.6 - - + +
107L LYS* 4.1 12.3 - - - -
127L MET 3.1 18.8 + - - +
128L PHE 3.2 2.0 + - - +
130L ALA* 1.3 73.6 - - - +
132L ALA* 1.3 58.2 + - - +
133L GLY* 3.1 6.6 + - - -
156L ASN 5.4 4.1 + - - -
158L LEU* 4.7 19.3 - - + +
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Residues in contact with ALA 132 (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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103L MET* 3.9 35.4 - - + +
104L TYR* 4.4 2.9 - - + +
107L LYS* 3.3 34.8 - - + +
110L PHE* 3.6 24.0 - - + +
111L LYS* 4.2 1.9 + - - +
128L PHE 2.9 12.1 + - - +
129L ALA 2.9 10.4 + - - +
131L LYS* 1.3 75.2 - - - +
133L GLY* 1.3 57.0 + - - +
134L ALA 3.7 0.2 - - - -
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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