Contacts of the helix formed by residues 123 - 132 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H SER* 3.0 19.3 + - - -
121H GLY 3.0 3.0 - - - -
122H THR* 1.3 79.2 - - - +
124H ILE* 1.3 64.9 + - - +
125H LEU 3.2 3.1 - - - -
126H SER* 3.1 13.1 + - - -
127H MET* 2.9 31.1 + - - +
149H SER* 4.2 6.1 - - - -
153H ILE* 4.9 8.5 - - - -
164H ILE* 5.4 0.2 - - - -
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Residues in contact with ILE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242G VAL* 4.0 15.3 - - + +
243G TYR* 4.4 2.0 - - + -
245G PHE* 3.7 29.2 - - + -
247G MET* 4.2 15.7 - - + -
90H LEU* 3.7 23.1 - - + -
95H ARG* 4.7 1.8 - - - +
96H THR* 4.5 3.1 - - + -
122H THR* 3.4 7.9 - - - +
123H GLY* 1.3 77.1 - - - +
125H LEU* 1.3 66.6 + - + +
127H MET* 3.3 9.3 + - + +
128H PHE* 3.0 54.1 + - + -
401H SAH 3.7 33.2 - - - +
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Residues in contact with LEU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H ARG* 5.6 3.6 - - - +
96H THR* 5.6 1.3 - - + -
99H TYR* 3.8 44.2 - - + -
103H MET* 3.8 2.9 - - + +
117H ASP* 3.3 19.0 + - - +
123H GLY 3.2 0.6 - - - -
124H ILE* 1.3 82.5 - - + +
126H SER* 1.3 63.0 + - - +
128H PHE* 3.2 21.4 + - + +
129H ALA 3.1 17.7 + - - -
183H ILE* 3.5 16.8 - - + +
184H SER* 4.2 5.2 - - - +
185H GLU* 3.9 23.1 - - + +
401H SAH 3.4 34.1 + - - +
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Residues in contact with SER 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H ASP* 2.8 35.7 + - - +
120H SER* 4.4 3.6 - - - -
123H GLY* 3.1 11.6 + - - -
125H LEU* 1.3 75.5 - - - +
127H MET* 1.3 57.2 + - - +
129H ALA* 3.3 3.0 + - - +
130H ALA* 3.0 23.4 + - - +
137H VAL* 3.6 24.0 - - - +
139H GLY* 4.3 7.8 - - - -
153H ILE* 5.3 0.4 - - - -
162H ILE* 3.5 24.6 - - - +
164H ILE* 4.8 1.3 - - - +
183H ILE* 4.4 3.4 - - - -
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Residues in contact with MET 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G PHE* 3.5 54.0 - - + -
247G MET* 4.4 6.7 - - + -
122H THR 5.1 0.2 - - - +
123H GLY 2.9 16.4 + - - +
124H ILE* 3.7 19.5 - - - +
126H SER* 1.3 74.4 - - - +
128H PHE* 1.3 63.0 + - - +
130H ALA* 3.6 1.8 + - - +
131H LYS* 3.1 29.1 + - - +
152H ILE* 3.8 22.0 - - + -
153H ILE* 4.0 17.7 - - + -
156H ASN* 4.0 14.6 - - - -
158H LEU* 3.8 9.3 - - + +
162H ILE* 3.7 20.4 - - + -
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Residues in contact with PHE 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243G TYR* 4.1 9.0 - + + -
245G PHE* 3.6 21.3 - + - -
96H THR* 3.7 28.5 - - + -
99H TYR 4.4 1.1 - - - -
100H ARG* 3.5 52.7 - - + -
103H MET* 3.7 14.8 - - + -
104H TYR* 3.4 25.1 - - + -
124H ILE* 3.0 39.7 + - + -
125H LEU* 3.2 25.3 + - + +
127H MET* 1.3 73.8 - - - +
129H ALA* 1.3 64.1 + - - +
131H LYS 3.3 1.0 + - - -
132H ALA* 3.0 21.3 + - - +
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Residues in contact with ALA 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H MET* 3.5 15.4 - - - -
110H PHE* 4.4 5.1 - - + -
115H VAL* 4.1 15.9 - - + -
125H LEU 3.1 13.3 + - - +
126H SER* 3.3 8.7 + - - +
128H PHE* 1.3 75.8 - - - +
130H ALA* 1.3 64.2 + - - +
132H ALA* 3.0 16.4 + - - +
133H GLY 3.4 0.7 + - - -
134H ALA* 3.4 16.9 + - - +
137H VAL* 4.0 13.5 - - + -
183H ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H SER 3.0 17.1 + - - +
127H MET 3.9 4.7 - - - +
128H PHE 3.3 0.2 - - - -
129H ALA* 1.3 75.8 - - - +
131H LYS* 1.3 59.0 + - - +
133H GLY* 3.0 21.0 + - - -
134H ALA 3.7 4.8 + - - +
137H VAL* 4.0 6.4 - - + +
158H LEU* 4.2 17.3 - - + -
161H ILE* 3.8 31.7 - - + +
162H ILE* 3.9 15.3 - - + -
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Residues in contact with LYS 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G PHE* 4.1 18.8 - - + -
104H TYR* 3.4 33.5 - - + +
107H LYS* 4.1 12.0 - - - -
127H MET 3.1 19.1 + - - +
129H ALA 3.2 0.2 - - - -
130H ALA* 1.3 76.3 - - - +
132H ALA* 1.3 57.1 + - - +
133H GLY 3.2 1.9 + - - -
156H ASN 5.3 4.9 + - - -
158H LEU* 4.7 20.2 - - + +
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Residues in contact with ALA 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H MET* 3.8 29.8 - - + +
104H TYR* 4.5 2.5 - - + +
107H LYS* 3.5 33.5 - - + +
110H PHE* 3.6 26.4 - - + +
111H LYS* 4.0 1.7 + - - +
128H PHE 3.0 13.7 + - - +
129H ALA 3.0 10.0 + - - +
131H LYS* 1.3 76.7 - - - +
133H GLY* 1.3 57.1 + - - +
134H ALA 3.7 1.1 - - - -
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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