Contacts of the helix formed by residues 123 - 132 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B SER* 2.9 18.4 + - - -
121B GLY 3.0 3.4 + - - -
122B THR* 1.3 78.7 - - - +
124B ILE* 1.3 65.2 + - - +
125B LEU 3.2 3.0 + - - -
126B SER* 3.2 13.0 + - - -
127B MET* 2.9 29.7 + - - +
149B SER* 4.3 7.0 - - - -
153B ILE* 4.8 8.3 - - - -
164B ILE* 5.3 0.4 - - - -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A VAL* 3.9 15.3 - - + +
243A TYR* 4.5 1.8 - - + -
245A PHE* 3.8 28.5 - - + -
247A MET* 4.2 14.6 - - + -
90B LEU* 3.7 22.7 - - + -
95B ARG* 4.6 2.7 - - - +
96B THR* 4.5 3.4 - - + -
120B SER 4.1 0.4 + - - -
122B THR* 3.4 8.0 + - - +
123B GLY* 1.3 77.5 - - - +
125B LEU* 1.3 64.8 + - + +
127B MET* 3.4 7.4 + - + +
128B PHE* 3.1 51.1 + - + -
401B SAH 3.4 34.8 - - - +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ARG* 5.4 3.1 - - - +
96B THR* 5.7 1.1 - - + -
99B TYR* 3.8 43.7 - - + -
103B MET* 3.9 2.7 - - + +
117B ASP* 3.4 19.2 + - - +
123B GLY 3.2 0.6 - - - -
124B ILE* 1.3 79.0 - - + +
126B SER* 1.3 66.0 + - - +
128B PHE* 3.1 22.7 + - + +
129B ALA 3.0 18.4 + - - -
183B ILE* 3.6 17.7 - - + +
184B SER* 4.3 4.5 - - - +
185B GLU* 3.9 22.9 - - + +
401B SAH 3.3 33.4 + - - +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 2.6 37.9 + - - +
120B SER* 4.5 2.3 - - - -
123B GLY* 3.2 10.9 + - - -
125B LEU* 1.3 75.7 - - - +
127B MET* 1.3 57.0 + - - +
129B ALA* 3.4 3.0 + - - +
130B ALA* 3.0 23.2 + - - +
137B VAL* 3.6 23.0 - - - +
139B GLY* 4.2 7.8 - - - -
153B ILE* 5.4 0.2 - - - -
162B ILE* 3.5 26.1 - - - +
164B ILE* 4.9 1.5 - - - +
183B ILE* 4.4 3.6 - - - -
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Residues in contact with MET 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PHE* 3.5 54.5 - - + -
247A MET* 4.3 8.1 - - + -
123B GLY 2.9 23.4 + - - +
124B ILE* 3.7 13.9 - - - +
126B SER* 1.3 74.0 - - - +
128B PHE* 1.3 64.8 + - - +
130B ALA* 3.7 1.4 - - - +
131B LYS* 3.1 28.6 + - - +
152B ILE* 3.9 20.6 - - + -
153B ILE* 4.1 13.5 - - + -
156B ASN* 3.8 15.5 - - - -
158B LEU* 3.8 16.1 - - + +
162B ILE* 3.8 15.3 - - + -
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A TYR* 4.1 9.4 - + + -
245A PHE* 3.7 22.2 - + - -
96B THR* 3.7 28.3 - - + -
99B TYR 4.4 0.9 - - - -
100B ARG* 3.4 53.2 - - + -
103B MET* 3.8 14.6 - - + -
104B TYR* 3.4 25.0 - - + -
124B ILE* 3.1 37.7 + - + -
125B LEU* 3.3 26.9 - - + +
127B MET* 1.3 76.1 - - - +
129B ALA* 1.3 62.0 + - - +
131B LYS 3.2 1.9 + - - -
132B ALA* 3.0 19.8 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B MET* 3.7 15.6 - - - -
110B PHE* 4.4 5.4 - - + +
115B VAL* 4.2 15.9 - - + -
125B LEU 3.0 11.7 + - - +
126B SER* 3.6 8.5 - - - +
127B MET 3.3 0.2 - - - -
128B PHE* 1.3 72.8 - - - +
130B ALA* 1.3 67.8 + - - +
132B ALA* 2.9 17.6 + - - +
133B GLY 3.4 6.4 + - - -
134B ALA* 3.4 10.9 + - - +
137B VAL* 4.1 12.6 - - + -
183B ILE* 4.1 13.5 - - + -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B SER 3.0 17.4 + - - +
127B MET* 3.7 5.6 - - - +
129B ALA* 1.3 75.7 - - - +
131B LYS* 1.3 58.9 - - - +
133B GLY* 3.1 18.9 + - - -
134B ALA* 3.7 5.2 + - - +
137B VAL* 4.0 7.3 - - + +
158B LEU* 4.2 16.3 - - + +
161B ILE* 3.9 28.7 - - + +
162B ILE* 3.9 17.9 - - + -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PHE* 4.2 18.6 - - + -
104B TYR* 3.5 30.9 - - + +
107B LYS* 4.2 12.0 - - - -
127B MET 3.1 19.0 + - - +
128B PHE 3.6 2.2 - - - +
130B ALA* 1.3 75.6 - - - +
132B ALA* 1.3 58.2 + - - +
133B GLY* 3.2 2.7 + - - -
156B ASN 5.4 3.2 + - - -
158B LEU* 4.6 21.1 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B MET* 3.7 32.5 - - + +
104B TYR* 4.5 2.2 - - + +
107B LYS* 3.4 40.1 - - + +
110B PHE* 3.7 19.4 - - + +
111B LYS* 4.1 1.7 + - - +
128B PHE 3.0 10.8 + - - +
129B ALA 2.9 11.4 + - - +
131B LYS* 1.3 76.0 - - - +
133B GLY* 1.3 57.8 + - - +
134B 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