Contacts of the strand formed by residues 72 - 78 (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 LEU 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 1.3 69.5 - - - +
73B GLU* 1.3 58.4 + - - +
99B LEU* 3.8 22.7 - - + -
100B CYS 3.9 2.0 - - - -
101B LEU* 4.1 6.1 - - + -
148B LEU* 3.6 18.6 - - + +
149B TRP* 3.3 50.5 - - - +
150B LEU* 3.9 12.7 - - + +
158B GLN* 3.1 29.7 + - + +
192B THR* 2.8 23.0 + - - -
193B PRO* 3.1 21.8 - - + +
207B ALA* 3.7 17.9 - - + -
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Residues in contact with GLU 73 (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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23B VAL 4.3 1.0 + - - +
71B GLU* 3.0 18.9 - - - +
72B LEU* 1.3 82.0 - - - +
74B LEU* 1.3 61.9 + - - +
99B LEU* 3.4 9.8 - - - +
100B CYS* 2.9 36.5 + - + +
102B ASP* 3.4 11.3 - - + +
148B LEU* 4.3 2.7 - - - -
189B LEU* 3.2 28.7 - - + +
191B GLY* 2.9 36.9 + - - +
192B THR* 3.7 6.2 - - - -
225B MG 2.1 32.8 - - - -
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Residues in contact with LEU 74 (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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27B TYR* 5.2 0.6 + - - -
73B GLU* 1.3 71.2 - - - +
75B GLY* 1.3 76.5 + - - +
76B VAL* 4.8 0.9 - - + -
97B TYR* 4.0 22.2 - - + -
98B ALA 4.1 3.6 - - - +
99B LEU* 4.6 2.9 - - - -
143B PRO* 3.9 22.0 - - + +
146B LEU* 4.1 15.3 - - + -
148B LEU* 3.9 20.3 - - + +
162B THR* 4.3 7.6 - - + -
165B MET* 4.4 6.1 - - + -
169B ILE* 4.0 22.2 - - + -
189B LEU* 3.7 0.6 - - - -
190B THR* 3.0 39.9 + - - +
191B GLY 4.4 1.6 + - - -
209B ILE* 4.1 23.3 - - + -
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Residues in contact with GLY 75 (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 3.6 1.8 + - - -
74B LEU* 1.3 74.8 - - - +
76B VAL* 1.3 62.6 + - - +
97B TYR* 3.4 15.6 - - - +
98B ALA 2.7 39.0 + - - +
100B CYS* 4.3 0.4 - - - -
187B ILE* 3.9 14.8 - - - -
188B ILE 3.4 6.7 - - - -
189B LEU* 4.1 8.3 - - - -
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Residues in contact with VAL 76 (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* 4.7 2.0 - - + +
75B GLY* 1.3 78.0 - - - +
77B VAL* 1.3 60.9 + - - +
78B MET* 3.7 11.8 + - - +
94B VAL* 4.0 33.9 - - + -
96B GLY 3.8 2.9 - - - -
97B TYR* 3.9 18.4 - - + -
169B ILE* 4.3 15.9 - - + -
173B ILE* 4.3 13.9 - - + -
186B ASP 3.8 0.2 - - - +
187B ILE* 3.3 8.1 - - - +
188B ILE* 2.9 40.1 + - + +
190B THR* 3.8 18.6 - - + -
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Residues in contact with VAL 77 (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* 4.0 13.0 - - + -
13B PHE* 3.8 57.4 - - + -
76B VAL* 1.3 72.6 - - - +
78B MET* 1.3 69.3 + - - +
94B VAL* 3.8 2.6 - - - +
95B GLY 2.9 21.0 + - - -
96B GLY 2.8 20.1 + - - +
97B TYR 4.2 13.7 - - - -
134B PHE* 4.0 9.9 - - + -
185B GLY* 4.3 3.4 - - - -
186B ASP 3.5 9.6 - - - +
187B ILE* 3.9 12.3 - - + +
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Residues in contact with MET 78 (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* 3.8 7.6 - - - +
76B VAL* 4.0 23.6 - - - +
77B VAL* 1.3 75.1 - - - +
79B GLY* 1.3 58.1 + - - +
80B LYS 4.6 4.0 - - - +
82B CYS* 4.0 10.8 - - + -
93B TYR* 3.4 31.6 - - + +
94B VAL* 4.7 0.9 - - - -
95B GLY* 3.7 1.3 - - - +
173B ILE* 3.8 30.7 - - + -
182B LEU* 4.0 25.1 - - + -
183B GLU 3.5 21.8 - - - +
184B GLU* 4.3 0.2 - - - -
185B GLY 2.9 23.8 + - - -
186B ASP 2.9 20.7 + - - +
187B ILE* 5.2 0.2 - - - -
188B ILE* 4.4 8.1 - - + -
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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