Contacts of the strand formed by residues 147 - 156 (chain B) in PDB entry 4STD
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 LEU 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B TRP* 3.7 23.3 - - + +
30B TYR* 4.7 1.3 - - - +
47B ARG 3.3 2.8 + - - -
48B ILE* 4.2 15.5 - - + -
49B ASP 3.0 25.1 + - - -
50B TYR* 4.1 19.7 - - + +
66B PHE* 4.7 4.0 - - + -
131B ASN* 3.9 2.7 - - - +
132B LEU 3.2 5.6 - - - -
133B HIS* 3.6 17.9 - - + -
134B TRP* 3.4 8.3 - - - -
144B PHE* 3.8 16.4 - - + -
146B GLY* 1.3 74.6 - - - +
148B LYS* 1.3 59.8 + - - +
149B PRO* 3.5 14.9 - - + +
174B BFS 3.4 33.7 - - - +
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Residues in contact with LYS 148 (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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49B ASP* 3.2 33.9 - - + +
51B ARG* 5.3 2.0 - - - +
130B ALA 3.7 2.1 - - - +
132B LEU* 2.6 61.3 + - + +
134B TRP* 3.5 20.5 - - + -
147B LEU* 1.3 71.9 - - - +
149B PRO* 1.3 65.2 - - - +
150B ASP* 3.4 6.5 + - + +
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Residues in contact with PRO 149 (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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49B ASP 3.4 16.4 - - - +
50B TYR* 4.0 14.8 - - + -
52B SER* 2.9 23.8 + - - -
53B PHE* 4.3 12.0 - - + -
131B ASN* 3.5 21.3 - - - +
147B LEU* 3.5 21.3 - - + +
148B LYS* 1.3 86.5 - - - +
150B ASP* 1.3 60.0 + - - +
151B ILE* 3.4 5.4 + - + +
174B BFS 3.3 30.3 - - + +
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Residues in contact with ASP 150 (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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52B SER* 3.6 12.0 + - - -
129B SER* 2.9 18.3 - - - -
130B ALA* 3.0 28.7 + - + +
131B ASN* 4.3 0.2 - - - +
148B LYS* 3.4 5.0 + - + +
149B PRO* 1.3 68.7 - - - +
151B ILE* 1.3 62.5 + - - +
152B ARG* 2.9 36.3 + - - +
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Residues in contact with ILE 151 (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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52B SER* 3.0 16.7 + - - +
53B PHE* 3.6 39.0 - - + -
127B ALA* 3.8 15.5 - - + -
128B HIS 4.2 2.0 - - - +
129B SER* 3.6 12.8 - - - -
149B PRO* 4.2 5.8 - - + +
150B ASP* 1.3 71.4 - - - +
152B ARG* 1.3 64.4 + - - +
153B TRP* 4.1 12.1 - - - +
158B PHE* 3.5 45.5 - - + -
174B BFS 4.0 18.2 - - + -
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Residues in contact with ARG 152 (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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128B HIS* 2.9 14.8 + - + +
129B SER 5.0 2.2 - - - -
130B ALA* 3.6 19.6 - - - +
150B ASP* 2.9 44.3 + - - -
151B ILE* 1.3 74.3 - - - +
153B TRP* 1.3 73.4 + - + +
28C ASP* 2.9 35.7 + - - -
31C ASP* 4.1 21.3 - - + +
32C SER* 2.9 28.5 + - - -
37C ARG* 4.4 0.4 - - - +
82C ARG* 3.7 25.8 + - - +
118C MET* 5.0 2.3 - - - +
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Residues in contact with TRP 153 (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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127B ALA* 3.8 2.1 - - - -
128B HIS* 3.0 70.3 + + + +
151B ILE* 3.6 8.2 - - - +
152B ARG* 1.3 93.8 - - + +
154B GLY* 1.3 80.8 + - - +
155B GLU* 4.3 4.5 - - + -
158B PHE* 5.8 0.7 - - - -
82C ARG* 3.6 34.5 - - + -
83C THR* 2.8 32.3 + - - +
109C PRO* 3.8 30.5 - - + -
111C GLN* 3.4 42.6 - - + -
113C TYR* 3.9 2.7 - - - -
118C MET* 4.3 13.0 - - + -
126C HIS* 5.4 1.8 - - - -
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Residues in contact with GLY 154 (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 HIS 3.3 11.0 - - - -
127B ALA* 4.4 0.4 - - - -
128B HIS* 3.9 0.7 - - - -
153B TRP* 1.3 83.6 - - - +
155B GLU* 1.3 63.2 - - - -
156B PHE 4.2 4.9 + - - +
158B PHE* 4.4 14.1 - - - -
111C GLN* 3.2 18.7 + - - -
113C TYR* 3.6 5.9 + - - -
118C MET* 5.7 0.2 - - - +
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Residues in contact with GLU 155 (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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107B ARG* 4.1 10.2 + - - -
125B GLY* 3.5 1.2 - - - -
126B HIS* 2.8 48.9 + - + +
128B HIS* 3.7 14.8 + - + -
153B TRP* 4.5 3.1 - - + -
154B GLY* 1.3 75.0 - - - -
156B PHE* 1.3 88.3 + - + +
157B ASP 3.4 0.5 + - - -
158B PHE 3.8 1.9 + - - -
107C ARG* 4.4 2.4 + - - -
109C PRO* 5.0 0.7 - - - +
111C GLN* 3.8 11.4 - - - +
124C LYS* 2.7 29.5 + - - +
126C HIS* 2.9 35.6 - - - -
156C PHE* 3.7 5.0 - - - -
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Residues in contact with PHE 156 (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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155A GLU* 3.8 4.0 - - - -
156A PHE* 4.7 9.0 - + - -
124B LYS* 3.5 47.8 - - + +
126B HIS* 3.3 41.3 - + - -
154B GLY 4.2 5.0 + - - +
155B GLU* 1.3 92.3 - - + +
157B ASP* 1.3 73.2 + - - +
158B PHE 3.8 1.2 + - - -
111C GLN* 4.7 3.0 + - - +
124C LYS* 3.6 22.8 - - - +
156C PHE* 4.7 6.7 - + - -
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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