Contacts of the strand formed by residues 81 - 89 (chain B) in PDB entry 4EEJ
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 HIS 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B ASP* 2.8 39.6 + - + -
72B GLU 3.3 8.5 + - - -
73B TYR* 3.6 38.2 + + + -
80B ARG* 1.3 74.6 - - - +
82B VAL* 1.3 82.1 + - - +
83B LYS* 4.7 7.9 + - + -
99B GLY* 4.6 8.0 - - - -
100B GLU 5.1 1.7 + - - -
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Residues in contact with VAL 82 (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* 3.6 1.6 - - - -
72B GLU* 2.9 62.1 + - + +
74B THR* 4.7 7.0 - - + -
80B ARG* 4.8 6.3 - - + -
81B HIS* 1.3 88.9 + - - +
83B LYS* 1.3 62.0 + - - +
84B ALA* 4.7 1.1 - - + -
97B GLN* 3.9 32.3 - - + +
98B LYS 3.3 13.7 - - - +
99B GLY* 4.4 7.9 - - - -
100B GLU 5.3 1.6 - - - +
101B LYS 6.3 0.2 - - - +
104B ARG* 4.1 25.8 - - - +
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Residues in contact with LYS 83 (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 GLU* 3.8 35.7 + - + +
70B PHE 3.6 2.9 - - - +
71B ASP* 2.6 38.6 + - - +
81B HIS* 4.7 7.5 + - + -
82B VAL* 1.3 73.1 - - - +
84B ALA* 1.4 57.6 - - - +
85B LEU* 5.3 0.5 - - - +
96B VAL* 3.6 2.6 - - - +
97B GLN* 3.6 1.0 - - - -
98B LYS* 2.8 53.2 + - + +
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Residues in contact with ALA 84 (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 GLU* 3.2 5.8 - - - +
70B PHE* 2.8 67.3 + - + +
72B GLU* 3.6 20.2 - - + +
82B VAL* 3.8 0.6 + - + -
83B LYS* 1.4 72.4 - - - +
85B LEU* 1.3 61.9 + - - +
95B CYS* 4.5 3.1 - - - -
96B VAL 3.3 4.9 - - - -
97B GLN* 4.1 12.8 - - + +
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Residues in contact with LEU 85 (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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67B GLY* 3.8 26.0 - - - +
68B VAL 3.9 0.9 - - - +
69B GLU* 3.8 33.0 - - + +
70B PHE* 4.6 1.8 - - - -
83B LYS 5.3 0.4 - - - +
84B ALA* 1.3 77.8 - - - +
86B VAL* 1.4 65.5 + - - +
87B THR* 4.0 17.7 + - + +
94B VAL 3.6 1.7 - - - +
95B CYS* 3.3 1.8 - - - -
96B VAL* 3.0 48.5 + - + +
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Residues in contact with VAL 86 (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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64B PHE* 3.6 46.0 - - + -
65B THR 5.3 1.0 + - - +
66B VAL* 3.4 5.2 - - + -
67B GLY 2.8 29.5 + - - +
68B VAL 5.1 1.4 + - - -
70B PHE* 4.2 9.2 - - + -
85B LEU* 1.4 74.6 - - - +
87B THR* 1.3 63.8 + - - +
93B LEU* 3.6 33.2 - - + -
94B VAL 3.2 7.9 - - - +
95B CYS* 3.8 20.4 - - + -
106B TRP* 3.9 14.1 - - + -
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Residues in contact with THR 87 (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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66B VAL* 4.2 6.7 - - + -
67B GLY* 4.5 8.5 - - - -
85B LEU* 4.0 28.1 + - + -
86B VAL* 1.3 79.7 - - - +
88B TRP* 1.3 68.3 + - - +
89B GLU* 4.8 5.4 + - - +
93B LEU* 3.6 8.4 - - - +
94B VAL* 2.8 42.9 + - - +
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Residues in contact with TRP 88 (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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2B ARG* 3.1 78.9 + - + +
4B ARG* 3.8 16.8 - - + -
44B GLN* 4.0 11.4 - - - -
47B ASP* 5.3 3.0 + - - -
49B PHE* 4.1 7.6 - + - -
66B VAL* 3.8 27.8 - - + +
87B THR* 1.3 77.9 - - - +
89B GLU* 1.3 64.3 + - - +
90B GLY 3.8 13.3 + - - +
91B ASP 3.9 1.8 - - - -
92B VAL 3.5 19.1 - - - -
93B LEU* 3.7 42.2 - - + -
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Residues in contact with GLU 89 (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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87B THR* 4.0 6.0 + - - +
88B TRP* 1.3 74.6 - - - +
90B GLY* 1.3 63.0 + - - +
91B ASP 3.2 0.9 + - - -
92B VAL* 2.9 30.8 + - + +
94B VAL* 3.6 38.7 - - + +
107B LYS* 4.9 8.4 + - - -
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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