Contacts of the helix formed by residues 93 - 105 (chain J) in PDB entry 1U8R
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 PRO 93 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115I ARG* 4.9 3.6 - - - -
91J GLY 3.7 5.4 - - - +
92J LEU* 1.3 95.6 - - + +
94J TRP* 1.3 66.5 + - - +
95J GLU* 3.8 15.0 - - - +
96J GLU* 3.0 50.5 + - + +
97J VAL* 3.3 9.5 + - - +
185J LYS* 5.5 2.0 - - - +
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Residues in contact with TRP 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J VAL* 4.3 13.7 - - + +
92J LEU 3.5 2.3 + - - -
93J PRO* 1.3 66.1 - - - +
95J GLU* 1.3 66.1 + - - +
96J GLU 2.7 16.6 + - - -
97J VAL* 3.1 23.4 + - - +
98J HIS 4.5 0.3 + - - -
127J PRO* 3.0 40.8 + - + +
128J PHE* 3.4 48.1 - + - -
170J LEU* 3.8 17.7 - - + -
181J ILE* 3.8 25.1 - - + -
184J LEU* 5.3 0.4 - - + -
185J LYS* 4.0 42.1 - - + +
189J VAL 4.9 0.4 - - - -
190J VAL* 4.2 15.3 - - + -
191J PRO* 4.4 11.7 - - + -
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Residues in contact with GLU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J PRO* 3.8 15.9 - - - +
94J TRP* 1.3 80.0 + - + +
96J GLU* 1.3 67.9 + - + +
98J HIS* 5.3 2.0 - - - -
99J ALA* 6.0 0.5 - - - +
128J PHE* 5.3 0.4 - - - -
178J ILE* 3.7 22.5 - - + +
181J ILE* 3.7 23.3 - - + +
182J THR* 3.5 34.5 - - + +
185J LYS* 3.1 28.9 + - - +
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Residues in contact with GLU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I ASP* 3.3 23.4 - - - +
92J LEU* 3.9 15.5 - - + +
93J PRO* 3.0 38.3 - - + +
94J TRP 2.7 8.7 + - - -
95J GLU* 1.3 93.4 - - + +
97J VAL* 1.3 61.4 + - - +
98J HIS* 3.4 2.6 + - - -
99J ALA* 3.7 10.1 + - - +
100J GLU* 3.5 19.2 + - - +
178J ILE* 5.3 5.4 - - + -
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Residues in contact with VAL 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J GLU* 4.3 10.3 - - + +
86J LEU* 3.3 36.4 - - + +
87J VAL* 3.3 30.5 - - + +
92J LEU* 3.8 11.2 - - + +
93J PRO 3.3 10.5 + - - +
94J TRP 3.1 15.7 - - - +
96J GLU* 1.3 75.0 - - - +
98J HIS* 1.3 65.8 + - - +
100J GLU* 3.0 2.9 + - - +
101J ALA* 2.7 36.9 + - - +
128J PHE* 3.7 21.3 - - + -
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Residues in contact with HIS 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ARG* 4.3 10.4 + - - -
79J HIS* 3.2 13.7 - + - -
83J GLU* 3.2 9.0 - - - +
94J TRP 4.5 1.0 + - - +
95J GLU 6.1 1.6 - - - -
96J GLU 3.4 1.5 - - - +
97J VAL* 1.3 84.7 - - + +
99J ALA* 1.3 61.4 + - + +
101J ALA 3.2 0.2 + - - -
102J CYS* 2.9 37.4 + - + +
128J PHE* 4.9 3.8 - - + -
172J GLU* 2.9 30.6 + - + -
175J GLN* 2.6 50.1 + - + +
176J GLY* 4.0 8.1 + - - -
8001J CO 2.1 22.4 + - - -
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Residues in contact with ALA 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J GLU 6.0 0.2 - - - +
96J GLU* 3.7 11.5 + - - +
97J VAL 3.3 0.8 - - - -
98J HIS* 1.3 84.0 - - + +
100J GLU* 1.3 62.0 + - - +
102J CYS* 3.7 15.7 + - - +
103J ARG* 3.1 23.7 + - - +
178J ILE* 6.3 2.9 - - + -
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Residues in contact with GLU 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I VAL 3.4 1.2 - - - +
108I MET* 3.7 0.7 - - - -
109I SER* 2.9 33.1 + - - -
112I VAL* 3.4 25.0 - - + +
86J LEU* 3.8 17.7 - - + -
92J LEU* 4.1 4.6 - - + +
96J GLU 3.5 11.6 + - - +
97J VAL 3.0 7.7 + - - +
99J ALA* 1.3 76.5 - - - +
101J ALA* 1.3 66.3 + - - +
103J ARG* 2.8 37.4 + - - +
104J TRP* 2.6 48.6 + - + +
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Residues in contact with ALA 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J HIS* 3.6 19.5 - - + +
82J ALA* 3.8 9.6 - - + -
83J GLU* 3.5 28.7 - - + +
86J LEU* 4.0 3.8 - - + +
97J VAL 2.7 19.8 + - - +
100J GLU* 1.3 70.3 - - - +
102J CYS* 1.3 55.7 + - - +
103J ARG 2.9 5.6 - - - -
104J TRP* 4.2 8.7 - - - +
105J GLU* 2.8 35.2 + - - +
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Residues in contact with CYS 102 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4J LEU 4.8 0.5 - - - +
5J VAL* 5.1 0.2 - - - +
10J MET* 4.0 9.9 - - - -
13J ARG* 3.4 22.4 - - - +
79J HIS* 3.7 3.6 + - + -
98J HIS* 2.9 26.8 + - + +
99J ALA* 3.8 11.7 - - - +
100J GLU 3.2 0.4 - - - -
101J ALA* 1.3 75.7 - - - +
103J ARG* 1.3 55.5 + - + +
105J GLU* 3.5 8.5 - - - -
106J HIS* 2.8 11.3 + - - -
8002J CO 1.9 46.8 + - - -
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Residues in contact with ARG 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I HIS 5.4 0.4 - - - -
107I VAL* 3.0 47.4 + - + +
109I SER* 3.8 12.1 - - - +
1J MET* 6.0 2.5 - - - -
3J GLU 5.4 4.0 - - - +
5J VAL* 4.0 17.5 - - + +
99J ALA* 3.1 20.8 + - - +
100J GLU* 2.8 43.9 + - - +
101J ALA 2.9 0.4 - - - -
102J CYS* 1.3 80.3 - - + +
104J TRP* 1.3 65.4 + - + +
105J GLU 3.2 1.6 - - - -
106J HIS* 3.2 22.3 + - - +
107J VAL* 4.3 1.9 + - - +
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Residues in contact with TRP 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85I LEU* 5.0 8.1 - - + -
104I TRP* 3.5 42.6 - + - -
107I VAL* 3.8 24.0 + - + +
108I MET* 4.1 18.0 - - + +
112I VAL* 3.9 21.8 - - + -
116I LEU* 5.7 0.2 - - + -
82J ALA* 4.6 18.4 - - + -
85J LEU* 4.4 15.3 - - + -
86J LEU* 3.9 23.1 - - + -
90J ILE* 5.1 2.9 - - + -
100J GLU* 2.6 48.8 + - + +
101J ALA* 3.9 6.5 - - - +
103J ARG* 1.3 74.5 - - - +
105J GLU* 1.3 64.2 + - - +
106J HIS 2.8 7.3 + - - -
107J VAL* 2.9 21.6 + - + +
108J MET* 3.1 24.3 + - + +
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Residues in contact with GLU 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J GLU* 4.0 5.9 - - - +
10J MET* 3.1 3.3 - - - +
13J ARG* 2.7 34.6 + - - -
75J VAL* 3.7 15.5 - - + +
78J LYS* 3.5 34.9 - - - +
79J HIS* 3.1 35.5 + - + +
82J ALA* 5.4 0.4 - - - +
101J ALA 2.8 9.9 + - - +
102J CYS* 2.9 11.6 - - - +
104J TRP* 1.3 76.1 - - - +
106J HIS* 1.3 78.2 + - + +
107J VAL 3.4 0.2 - - - -
8002J CO 2.0 29.7 + - - -
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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