Contacts of the strand formed by residues 68 - 75 (chain B) in PDB entry 4HUG
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 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B SER* 1.3 74.5 - - - +
69B SER* 1.3 58.6 + - - +
70B VAL* 3.7 27.8 - - + -
85B GLY* 4.2 0.9 - - - -
86B VAL 3.4 11.4 - - - +
87B ASP* 4.9 0.4 - - - +
88B THR* 3.5 2.9 + - - -
94B LEU* 4.1 11.2 - - + -
95B PHE* 3.8 19.5 - - + -
116B GLY* 4.7 1.8 - - - +
119B TYR* 3.7 35.7 - - + -
120B LEU* 3.9 19.7 - - + -
127B LYS* 4.0 7.4 - - + +
128B PRO 2.8 11.8 + - - +
129B ILE* 3.2 14.1 - - + -
130B TYR* 2.7 32.4 + - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 1.3 73.6 - - - +
70B VAL* 1.3 64.1 + - - +
71B ASP 4.3 0.2 + - - -
84B LYS 3.9 0.3 - - - +
85B GLY* 3.4 2.3 - - - -
86B VAL* 2.8 49.1 + - - +
88B THR* 2.7 29.1 + - - +
130B TYR* 3.5 16.6 - - - +
181B TRP* 4.2 2.9 - - - -
189B ILE* 3.8 22.4 - - - +
190B LYS* 4.4 5.8 - - - +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.7 20.2 - - + -
69B SER* 1.3 77.5 - - - +
71B ASP* 1.3 61.9 + - - +
84B LYS 3.4 3.8 - - - +
85B GLY* 4.1 2.2 - - - -
95B PHE* 3.9 10.5 - - + -
109B GLU* 4.6 7.8 - - - +
112B ALA* 3.6 40.6 - - + +
113B ILE* 4.2 11.7 - - + -
116B GLY* 5.2 0.2 - - - -
129B ILE* 4.4 6.7 - - + -
130B TYR 3.0 20.8 + - - +
131B SER* 4.1 18.4 - - - +
132B ASN 4.8 0.7 + - - -
189B ILE* 3.2 22.1 - - - +
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Residues in contact with ASP 71 (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 SER 4.9 0.2 - - - +
70B VAL* 1.3 77.3 - - - +
72B VAL* 1.3 69.5 + - - +
83B TYR* 3.2 4.7 - - - +
84B LYS* 3.0 64.3 + - - +
86B VAL* 4.6 2.1 - - - +
109B GLU* 4.9 2.0 - - - -
189B ILE* 3.5 22.9 - - + +
190B LYS 3.8 15.9 - - - +
191B ALA* 4.8 2.9 - - - -
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASP* 1.3 85.9 - - - +
73B GLY* 1.3 63.6 + - - +
74B SER* 4.0 1.1 + - - +
81B VAL* 3.5 24.5 - - + -
82B GLU 3.3 11.2 - - - +
83B TYR* 3.9 7.6 - - + -
105B ASN* 3.7 25.5 + - - +
108B GLY 3.5 8.3 - - - +
109B GLU* 3.4 53.7 + - - +
112B ALA* 4.4 2.5 - - + -
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Residues in contact with GLY 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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71B ASP 4.3 0.4 + - - -
72B VAL* 1.3 74.1 - - - +
74B SER* 1.3 61.9 + - - -
75B GLN* 5.8 0.7 - - - -
80B ILE 3.7 0.7 - - - +
81B VAL* 3.4 4.7 - - - +
82B GLU* 2.9 45.9 + - - +
83B TYR* 4.7 0.4 - - - +
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Residues in contact with SER 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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72B VAL* 4.0 3.9 + - - +
73B GLY* 1.3 76.0 + - - -
75B GLN* 1.3 65.4 + - - +
76B GLY 3.6 19.6 + - - -
77B ASN* 5.3 2.0 - - - -
80B ILE 3.3 5.4 - - - -
81B VAL* 4.2 4.6 - - - +
105B ASN* 2.9 42.2 + - - +
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Residues in contact with GLN 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 GLY 5.8 0.9 - - - -
74B SER* 1.3 74.4 - - - +
76B GLY* 1.3 61.1 + - - +
79B GLY* 3.3 3.6 - - - -
80B ILE* 2.9 68.0 + - + +
82B GLU* 4.4 13.4 + - - +
99B PRO* 5.6 1.2 - - - +
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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