Contacts of the strand formed by residues 119 - 127 (chain B) in PDB entry 3SBW
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 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 4.7 4.9 - - - -
70B LEU 5.7 1.6 - - - -
117B ASP 3.2 4.6 + - - -
118B SER* 1.3 74.2 - - - +
120B ILE* 1.3 64.6 + - - -
121B TYR* 3.5 9.7 - - - -
141B GLU* 3.5 4.7 - - - -
142B LEU 2.8 34.7 + - - -
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Residues in contact with ILE 120 (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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69B ARG* 3.7 3.7 - - - +
70B LEU* 2.9 62.5 + - + -
119B GLY* 1.3 72.8 - - - -
121B TYR* 1.3 68.0 + - - +
139B GLY* 3.7 21.8 - - - -
140B ALA 3.2 8.1 - - - +
141B GLU* 3.6 39.9 - - + +
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Residues in contact with TYR 121 (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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37B PHE* 3.3 16.8 - - + -
52B PHE* 5.0 6.5 - + + -
67B TRP* 3.6 23.1 - + - +
68B ASN 3.2 17.9 - - - +
69B ARG* 3.6 35.2 + - + +
70B LEU* 4.7 0.4 - - - +
79B GLN* 4.3 2.9 - - + -
95B PHE* 3.7 30.1 - + - -
110B ILE* 4.7 1.8 - - + -
117B ASP* 2.7 35.1 + - - +
119B GLY* 3.5 19.3 - - - -
120B ILE* 1.3 79.0 - - - +
122B LEU* 1.3 62.3 + - - +
139B GLY* 3.2 5.4 - - - -
140B ALA 2.8 34.2 + - - +
142B LEU* 4.0 19.5 - - + -
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Residues in contact with LEU 122 (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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37B PHE* 3.7 10.5 - - - -
67B TRP* 3.6 5.2 - - - -
68B ASN* 2.8 50.5 + - + +
70B LEU* 4.4 20.4 - - + -
76B THR* 4.7 0.4 - - + -
121B TYR* 1.3 76.9 - - - +
123B CYS* 1.3 75.8 - - - +
136B GLU* 3.8 29.2 - - + +
137B SER* 3.7 27.8 - - - +
138B PRO 4.1 3.4 - - - +
139B GLY* 4.2 7.6 - - - +
123C TYR* 3.9 5.8 - - - +
125C ARG* 4.2 12.1 - - - +
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Residues in contact with CYS 123 (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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35B LEU* 4.0 4.4 - - - +
36B THR 4.3 1.3 - - - -
37B PHE* 3.9 9.7 - - + -
54B CYS* 2.0 50.0 - - + -
65B LEU* 4.4 1.8 - - + -
66B ASN 3.2 6.1 - - - +
108B MET* 3.5 22.7 - - + -
122B LEU* 1.3 82.8 - - - +
124B GLY* 1.3 58.4 + - - +
137B SER* 3.0 44.2 + - - -
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Residues in contact with GLY 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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35B LEU* 4.3 0.9 - - - -
64B MET 3.7 0.9 - - - +
65B LEU* 3.4 6.5 - - - +
66B ASN* 2.7 44.2 + - - +
68B ASN* 4.7 0.6 - - - +
122B LEU* 4.3 0.8 - - - +
123B CYS* 1.3 75.7 - - - +
125B ALA* 1.3 61.1 + - - -
126B ILE* 5.4 0.2 - - - -
135B GLU 3.1 11.7 - - - -
136B GLU* 4.3 0.7 - - - -
123C TYR* 4.2 19.9 + - - -
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Residues in contact with ALA 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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35B LEU* 4.0 7.0 - - + +
56B LEU* 4.3 17.0 - - + -
59B TRP* 6.4 0.2 - - + -
63B LEU* 4.1 25.8 - - + -
64B MET 3.4 6.7 - - - +
65B LEU* 4.4 3.1 - - + -
124B GLY* 1.3 73.7 - - - -
126B ILE* 1.3 62.3 + - - +
127B SER* 4.0 3.1 + - - +
133B LYS 3.5 1.9 - - - +
134B ILE* 3.5 5.5 - - - +
135B GLU* 2.8 43.2 + - + +
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Residues in contact with ILE 126 (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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62B ASP 4.9 0.5 - - - +
63B LEU* 3.9 6.0 - - - -
64B MET* 2.9 41.1 + - + +
66B ASN* 3.2 35.9 - - - +
124B GLY 5.2 0.2 - - - +
125B ALA* 1.3 76.1 - - - +
127B SER* 1.3 63.9 + - - +
128B LEU* 3.9 27.1 + - + +
133B LYS 3.4 6.5 - - - +
134B ILE* 4.8 3.8 - - + -
115C MET* 4.1 22.7 - - + -
121C ALA* 4.5 20.0 - - + -
122C ASP 4.6 3.8 - - - +
123C TYR* 3.9 25.6 - - + -
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Residues in contact with SER 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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62B ASP 6.0 0.2 - - - -
63B LEU* 3.3 26.4 - - - +
125B ALA* 4.8 3.6 + - - +
126B ILE* 1.3 75.1 - - - +
128B LEU* 1.3 66.5 + - - +
129B HIS 4.5 8.3 - - - -
131B LYS 3.6 13.9 - - - -
132B LEU* 3.2 5.7 - - - +
133B LYS* 2.8 46.3 + - - +
135B GLU* 5.9 1.2 - - - +
115C MET* 5.4 0.7 - - - +
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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