Contacts of the strand formed by residues 94 - 101 (chain B) in PDB entry 1SAW
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 VAL 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B VAL* 4.0 13.7 - - + -
77B VAL 3.8 5.2 - - - +
78B MET* 4.4 2.7 - - + +
79B GLY* 3.8 2.0 - - - -
90B ALA 3.9 2.9 - - - +
91B MET* 3.6 26.5 - - + +
92B ASP 3.4 2.3 - - - +
93B TYR* 1.3 79.9 - - - +
95B GLY* 1.3 62.5 + - - +
96B GLY* 3.5 24.5 - - - +
97B TYR* 4.1 17.5 - - + +
137B LYS* 2.8 33.4 + - + +
173B ILE* 3.5 32.3 - - + -
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Residues in contact with GLY 95 (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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10B LEU* 3.9 14.6 - - - +
77B VAL 2.9 10.4 + - - -
79B GLY* 3.2 20.7 - - - +
94B VAL* 1.3 74.7 - - - +
96B GLY* 1.3 58.9 + - - +
134B PHE* 3.5 14.4 - - - -
136B PRO* 4.2 0.5 - - - +
137B LYS* 3.3 19.5 + - - +
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Residues in contact with GLY 96 (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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77B VAL 2.8 25.7 + - - +
94B VAL* 3.5 9.2 - - - +
95B GLY* 1.3 80.9 - - - +
97B TYR* 1.3 74.3 - - - -
134B PHE* 3.5 10.9 - - - -
135B VAL 3.3 11.7 - - - -
137B LYS* 3.8 8.3 - - - -
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Residues in contact with TYR 97 (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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74B LEU* 4.0 16.2 - - + -
75B GLY 3.4 20.0 - - - +
76B VAL* 3.9 24.2 - - + -
77B VAL* 4.2 6.1 - - - -
91B MET* 3.2 30.1 - - - +
94B VAL* 4.1 10.7 - - + +
96B GLY* 1.3 83.3 - - - -
98B ALA* 1.3 61.8 + - - +
134B PHE* 3.7 4.3 - - - -
135B VAL* 2.8 40.2 + - + +
137B LYS* 4.4 10.8 - - + +
140B ILE* 3.5 49.3 + - + -
143B PRO* 3.3 29.4 - - + +
169B ILE* 4.4 2.9 - - + -
209B ILE* 5.7 1.1 - - + -
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Residues in contact with ALA 98 (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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13B PHE* 3.6 33.7 - - + -
74B LEU* 4.1 4.8 - - - -
75B GLY* 2.7 41.7 + - - -
77B VAL* 4.3 0.4 - - - +
97B TYR* 1.3 78.8 - - - +
99B LEU* 1.3 57.6 + - - +
100B CYS* 3.7 0.6 - - - -
131B VAL* 4.0 11.4 - - + -
132B SER* 3.8 11.9 - - - +
133B ALA 4.2 3.8 - - - +
135B VAL* 5.3 2.2 - - - -
187B ILE* 4.4 5.8 - - + -
209B ILE* 5.1 1.1 - - - -
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Residues in contact with LEU 99 (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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72B LEU* 3.8 26.5 - - + -
73B GLU 3.4 21.8 - - - +
74B LEU* 4.4 0.9 - - - +
98B ALA* 1.3 71.4 - - - +
100B CYS* 1.3 60.9 + - - +
131B VAL* 3.6 1.0 - - - -
132B SER* 2.9 42.8 + - - +
148B LEU* 4.2 11.7 - - + -
207B ALA* 3.7 11.2 - - + +
208B GLY* 3.5 40.8 - - - +
209B ILE* 4.1 28.1 - - + +
213B VAL* 4.4 3.6 - - + +
215B MET* 3.6 12.4 - - + +
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Residues in contact with CYS 100 (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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73B GLU* 2.9 33.5 + - - +
75B GLY* 4.1 1.6 - - - -
98B ALA 3.7 13.5 - - - -
99B LEU* 1.3 80.5 - - - +
101B LEU* 1.3 71.0 - - - +
102B ASP 4.2 0.4 - - - -
129B CYS* 4.0 7.4 - - - -
130B PRO 3.2 11.4 - - - +
131B VAL* 4.3 11.0 - - - -
187B ILE* 3.7 15.5 - - - -
189B LEU* 3.4 42.4 - - + -
215B MET* 4.2 0.7 - - - -
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Residues in contact with LEU 101 (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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59B ILE* 4.0 21.3 - - + -
70B HIS* 5.2 1.1 - - + -
71B GLU 3.2 10.5 - - - +
72B LEU* 4.1 8.3 - - + -
100B CYS* 1.3 85.4 - - - +
102B ASP* 1.3 60.4 + - - +
103B MET* 3.2 18.8 + - - -
129B CYS* 3.3 9.9 - - - +
130B PRO* 3.0 34.0 + - + +
150B LEU* 3.6 28.0 - - + -
189B LEU* 4.9 0.4 - - - -
205B ILE* 3.9 25.6 - - + -
207B ALA* 4.6 2.0 - - + -
215B MET* 3.5 24.0 - - + -
217B PHE* 4.7 3.8 - - + -
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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