Contacts of the helix formed by residues 72 - 82 (chain B) in PDB entry 5UHE
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 ASP 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B GLU 4.2 1.0 - - - +
63B PHE 3.9 13.2 - - - +
65B THR* 3.4 26.7 - - + +
66B VAL 5.7 0.2 - - - -
70B LYS 3.9 1.0 + - - -
71B GLU* 1.3 78.0 - - - +
73B VAL* 1.3 95.3 + - - +
74B THR* 3.1 26.9 + - - +
75B GLU* 3.4 16.3 + - - +
76B ILE* 3.1 16.9 + - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 4.7 7.9 - - + +
59B VAL* 4.7 7.2 - - + -
62B GLU* 3.2 47.1 - - + +
64B THR 3.2 17.9 - - - +
65B THR* 4.1 6.2 - - - +
66B VAL* 4.5 14.3 - - + +
72B ASP* 1.3 86.3 + - - +
74B THR* 1.3 63.1 + - + +
76B ILE* 3.6 11.2 + - - +
77B ILE* 3.1 38.0 + - + +
162B ILE* 4.7 12.8 - - + -
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Residues in contact with THR 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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62B GLU 6.0 0.7 - - - +
72B ASP* 3.7 22.6 + - - +
73B VAL* 1.3 80.3 - - + +
75B GLU* 1.3 77.8 + - - +
77B ILE* 3.0 28.8 + - + +
78B LEU* 3.3 12.9 - - - +
608D GLU* 3.1 40.6 - - + +
611D VAL* 5.2 10.1 - - - -
663D MET* 5.8 2.3 - - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU* 3.9 19.3 - - + +
72B ASP* 3.4 24.0 + - - +
74B THR* 1.3 88.9 + - - +
76B ILE* 1.3 55.6 + - - +
78B LEU* 3.5 6.0 + - - -
79B ASN* 2.5 36.5 + - - +
636D ARG* 3.5 21.3 + - - +
663D MET* 4.1 28.9 - - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 6.0 2.5 - - + -
56B ILE* 5.6 8.5 - - + -
66B VAL* 4.6 15.5 - - + -
69B VAL* 4.2 15.9 - - + -
71B GLU* 3.8 24.9 - - + +
72B ASP 3.1 21.5 - - - +
73B VAL* 3.8 10.8 - - - +
74B THR 3.1 0.6 - - - -
75B GLU* 1.3 76.1 - - - +
77B ILE* 1.3 66.0 + - + +
79B ASN* 3.3 8.8 + - - +
80B LEU* 3.1 33.5 + - + +
125B ILE* 4.3 20.0 - - + -
126B ALA* 4.7 8.3 - - + -
134B LEU* 6.1 3.1 - - + -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.6 16.2 - - + -
56B ILE* 6.4 0.2 - - + -
62B GLU* 6.1 0.2 - - + -
73B VAL* 3.1 34.1 - - + +
74B THR* 3.0 12.5 + - + +
76B ILE* 1.3 77.8 - - + +
78B LEU* 1.3 58.4 + - + +
80B LEU* 3.1 10.5 + - - +
81B LYS* 2.9 51.6 + - - +
162B ILE* 4.6 15.7 - - + -
163B PRO 5.9 0.9 - - - +
164B VAL* 4.0 20.0 - - + -
607D PRO* 5.6 6.7 - - + -
608D GLU* 6.2 2.5 - - + +
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Residues in contact with LEU 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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74B THR* 3.3 16.5 + - - +
75B GLU* 3.8 11.9 - - - +
76B ILE 3.2 0.4 - - - -
77B ILE* 1.3 80.5 - - + +
79B ASN* 1.3 64.9 + - - +
80B LEU 3.3 0.3 + - - -
81B LYS* 3.4 16.1 + - - +
82B SER* 3.5 10.0 + - - -
611D VAL* 3.6 39.3 - - + +
612D TYR 3.2 26.0 - - - +
613D SER* 3.6 26.9 - - - -
636D ARG* 4.4 20.4 + - + +
663D MET* 4.1 21.5 - - + -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLU* 5.1 4.6 - - - +
75B GLU* 2.5 28.1 + - - +
76B ILE 3.3 6.3 + - - +
78B LEU* 1.3 77.3 - - - +
80B LEU* 1.3 59.6 + - - +
82B SER* 3.5 8.3 + - - -
123B MET* 3.2 32.9 - - - +
124B HIS* 3.7 29.4 - - - +
125B ILE* 3.6 24.3 + - + +
636D ARG* 2.8 29.0 + - - +
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Residues in contact with LEU 80 (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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51B VAL* 4.4 18.3 - - + +
54B ILE* 4.2 26.0 - - + -
76B ILE* 3.1 26.9 + - + +
77B ILE* 3.4 9.9 - - - +
78B LEU 3.1 0.4 - - - -
79B ASN* 1.3 75.8 - - - +
81B LYS* 1.3 65.1 + - - +
82B SER 3.1 2.2 - - - -
83B LEU* 3.1 37.2 + - + +
97B LEU* 6.0 2.2 - - + -
110B ILE* 5.6 0.9 - - + -
123B MET* 5.2 0.4 - - + -
125B ILE* 4.5 25.4 - - + -
136B VAL* 5.1 4.7 - - + -
138B LEU* 4.1 31.0 - - + -
164B VAL* 6.0 3.1 - - + -
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Residues in contact with LYS 81 (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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50B ALA* 5.6 4.0 - - - +
51B VAL* 5.9 3.6 - - - -
77B ILE* 2.9 39.2 + - - +
78B LEU* 3.4 17.4 + - - +
80B LEU* 1.3 76.4 - - - +
82B SER* 1.3 60.1 + - - +
83B LEU 3.3 6.6 + - - +
164B VAL* 4.0 18.4 - - + +
165B ASP* 2.5 45.6 + - + +
167B ILE* 4.2 27.6 - - + +
199B LYS* 5.1 5.7 + - - -
611D VAL 2.9 24.5 + - - -
613D SER* 4.5 4.5 - - - -
617D GLU* 3.6 23.4 + - - +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU 3.5 8.7 + - - -
79B ASN* 3.7 11.7 - - - -
80B LEU 3.1 1.2 - - - -
81B LYS* 1.3 78.8 - - - +
83B LEU* 1.3 60.7 + - - +
84B VAL* 3.5 10.5 + - - +
120B ASN* 3.7 10.9 + - - -
123B MET* 4.0 11.4 - - - -
167B ILE* 6.0 0.2 - - - -
199B LYS* 6.1 1.8 - - - +
613D SER* 5.1 8.9 - - - -
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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