Contacts of the helix formed by residues 123 - 132 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I SER* 3.2 13.8 + - - -
121I GLY 3.0 7.6 - - - -
122I THR* 1.3 77.7 - - - +
124I ILE* 1.3 65.1 + - - +
125I LEU 3.2 3.5 + - - -
126I SER* 3.3 10.5 + - - -
127I MET* 2.9 29.7 + - - +
149I SER* 4.1 7.9 - - - -
153I ILE* 4.7 10.9 - - - +
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Residues in contact with ILE 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I LEU* 3.9 22.2 - - + -
95I ARG* 4.7 2.0 - - - +
96I THR* 4.5 2.9 - - + -
120I SER 4.3 0.4 + - - -
122I THR* 3.4 6.7 - - - +
123I GLY* 1.3 77.1 - - - +
125I LEU* 1.3 72.0 + - + +
127I MET* 3.2 14.9 + - + +
128I PHE* 3.0 60.4 + - + -
401I SAH 3.6 34.8 - - - +
242J VAL* 4.2 15.5 - - + +
243J TYR* 4.5 1.8 - - + -
245J PHE* 3.9 19.7 - - + -
247J MET* 4.3 10.3 - - + -
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Residues in contact with LEU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I ARG* 5.5 3.1 - - - +
96I THR* 5.6 1.1 - - + -
99I TYR* 3.7 46.2 - - + -
103I MET* 3.7 3.5 - - + +
117I ASP* 3.3 19.6 + - - +
120I SER 4.9 0.6 + - - -
123I GLY 3.3 0.6 - - - -
124I ILE* 1.3 85.8 - - + +
126I SER* 1.3 57.3 + - - +
128I PHE* 3.2 20.6 + - + +
129I ALA 3.0 22.7 + - - -
183I ILE* 3.6 16.9 - - + +
184I SER* 4.2 6.1 - - - +
185I GLU* 3.8 22.4 - - + +
401I SAH 3.5 32.8 - - - +
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Residues in contact with SER 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I ASP* 2.8 36.1 + - - +
120I SER* 4.6 1.7 - - - -
123I GLY* 3.3 11.2 + - - -
125I LEU* 1.3 75.0 - - - +
127I MET* 1.3 61.9 + - - +
129I ALA* 3.3 4.5 + - - +
130I ALA* 2.9 28.9 + - - +
137I VAL* 3.5 22.4 - - - +
139I GLY* 4.5 5.4 - - - -
162I ILE* 3.6 21.5 - - - +
164I ILE* 5.3 1.6 - - - -
183I ILE* 4.4 1.3 - - - -
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Residues in contact with MET 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I GLY 2.9 15.5 + - - +
124I ILE* 3.5 16.6 - - - +
126I SER* 1.3 72.3 - - - +
128I PHE* 1.3 64.7 + - - +
130I ALA* 3.4 1.6 + - - +
131I LYS* 3.0 28.8 + - - +
152I ILE* 3.8 20.9 - - + -
153I ILE* 4.0 13.5 - - + -
156I ASN* 3.9 14.6 - - - -
158I LEU* 3.8 10.5 - - + +
162I ILE* 3.8 20.0 - - + -
245J PHE* 3.6 55.9 - - + -
247J MET* 4.1 13.7 - - + -
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Residues in contact with PHE 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I THR* 3.8 29.4 - - + -
99I TYR 4.3 1.3 - - - -
100I ARG* 3.4 55.6 - - + -
103I MET* 3.5 13.9 - - + -
104I TYR* 3.4 23.6 - - + -
124I ILE* 3.0 46.9 + - + -
125I LEU* 3.2 24.7 + - + +
127I MET* 1.3 71.0 - - - +
129I ALA* 1.3 66.3 + - - +
131I LYS 3.1 2.1 + - - -
132I ALA* 2.9 21.1 + - - +
243J TYR* 4.0 10.3 - + + -
245J PHE* 3.8 12.6 - + - -
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Residues in contact with ALA 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I MET* 3.3 15.0 - - - -
110I PHE* 4.5 6.6 - - + +
115I VAL* 4.2 15.3 - - + -
125I LEU 3.0 12.3 + - - +
126I SER* 3.3 8.5 + - - +
128I PHE* 1.3 77.6 - - - +
130I ALA* 1.3 62.6 + - - +
132I ALA* 3.0 16.8 + - - +
133I GLY 3.3 7.8 + - - -
134I ALA* 3.4 9.7 + - - +
137I VAL* 4.0 13.9 - - + -
183I ILE* 4.1 13.2 - - + -
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Residues in contact with ALA 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I SER 2.9 17.1 + - - +
127I MET* 3.8 4.5 - - - +
129I ALA* 1.3 75.0 - - - +
131I LYS* 1.3 58.5 + - - +
133I GLY* 2.9 21.0 + - - -
134I ALA 3.8 4.9 + - - +
137I VAL* 4.0 6.2 - - + +
158I LEU* 4.2 16.4 - - + -
161I ILE* 3.7 33.5 - - + +
162I ILE* 4.0 14.6 - - + -
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Residues in contact with LYS 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I TYR* 3.4 34.0 - - + +
107I LYS* 4.1 11.6 - - - -
127I MET 3.0 17.7 + - - +
130I ALA* 1.3 77.6 - - - +
132I ALA* 1.3 57.7 + - - +
133I GLY* 3.1 1.9 + - - -
156I ASN 5.6 2.6 + - - -
158I LEU* 4.7 19.1 - - + +
245J PHE* 3.9 21.3 - - + -
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Residues in contact with ALA 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I MET* 3.8 34.1 - - + +
104I TYR* 4.3 3.3 - - + +
107I LYS* 3.4 32.5 - - + +
110I PHE* 3.5 25.5 - - + +
111I LYS* 4.2 1.4 + - - +
128I PHE 2.9 12.2 + - - +
129I ALA 3.0 10.7 + - - +
131I LYS* 1.3 77.6 - - - +
133I GLY* 1.3 54.9 + - - +
134I ALA 3.7 0.4 - - - -
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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