Contacts of the helix formed by residues 75 - 90 (chain J) in PDB entry 5U07
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 75 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B HIS* 6.2 0.4 - - - -
211B ARG* 2.9 37.3 + - - -
39J PRO* 4.5 11.6 - - + +
74J VAL* 1.3 87.0 - - + +
76J ALA* 1.3 66.5 + - - +
77J VAL* 3.0 3.9 + - - -
78J GLU* 3.4 21.5 + - - +
79J ARG* 3.5 20.4 + - + -
169J LEU* 5.7 2.3 - - + +
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Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J VAL* 2.7 6.3 + - + +
75J HIS* 1.3 83.5 + - - +
77J VAL* 1.3 67.2 + - - +
79J ARG* 3.0 8.8 - - - +
80J ALA* 2.9 14.1 + - - +
169J LEU* 3.6 37.2 - - + +
199J LEU 5.0 1.1 - - - +
200J ALA 4.9 3.4 - - - +
203J GLY* 3.6 28.0 - - - +
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Residues in contact with VAL 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ILE* 5.4 4.7 - - + -
55J VAL* 4.8 5.4 - - + -
56J PRO* 3.8 20.4 - - + +
74J VAL* 2.7 32.0 + - - +
75J HIS* 3.9 2.9 - - - +
76J ALA* 1.3 74.0 - - - +
78J GLU* 1.3 67.1 + - + +
80J ALA* 2.0 48.4 + - + +
81J PHE* 3.2 33.1 + - + -
200J ALA* 4.6 20.7 + - + +
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Residues in contact with GLU 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 3.5 24.4 + - - -
215B GLN* 2.4 34.6 + - - +
219B ARG* 5.0 2.6 + - - -
39J PRO* 4.1 3.6 - - - +
55J VAL* 3.5 32.3 - - + +
75J HIS* 3.7 16.1 - - - +
77J VAL* 1.3 86.5 - - + +
79J ARG* 1.3 62.2 + - - +
81J PHE* 3.4 3.3 + - - +
82J TYR* 3.0 58.8 + - + -
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Residues in contact with ARG 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J GLY 5.3 0.6 + - - -
36J GLY* 3.8 6.3 + - - +
37J LEU* 2.3 51.8 + - - +
38J ALA* 3.8 6.1 - - - +
39J PRO* 3.3 26.8 - - - +
44J MET* 4.7 0.8 - - - +
75J HIS* 3.5 16.1 + - + +
76J ALA* 3.0 17.2 + - - +
77J VAL 2.4 8.9 + - - -
78J GLU* 1.3 73.6 - - - +
80J ALA* 1.3 60.0 + - - +
82J TYR* 3.9 2.4 - - - +
83J ALA* 2.9 38.9 + - - +
169J LEU* 4.2 11.4 + - + +
170J ASP* 4.7 15.6 + - - +
173J HIS* 3.4 46.0 + - + +
174J ARG* 6.1 0.6 - - - +
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Residues in contact with ALA 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J ALA 2.9 5.3 + - - +
77J VAL* 2.0 33.5 + - + +
79J ARG* 1.3 69.7 - - - +
81J PHE* 1.3 63.1 + - + +
83J ALA* 3.1 8.5 + - - +
84J VAL* 3.1 17.0 + - - +
173J HIS* 3.5 12.0 - - - -
196J ILE* 4.2 8.5 - - + +
199J LEU* 3.6 40.5 - - + +
200J ALA* 3.7 6.3 - - + +
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Residues in contact with PHE 81 (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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6J ILE* 4.1 16.6 - - + -
9J HIS* 4.2 4.9 - - + -
10J ALA* 3.6 29.4 - - - -
13J LEU* 3.3 29.5 - - + +
51J VAL* 6.1 0.7 - - + +
54J TYR* 4.5 2.2 - - + -
55J VAL* 4.3 13.7 - - + -
56J PRO* 2.9 36.6 - - + -
77J VAL* 3.2 29.1 + - + -
78J GLU* 3.9 4.9 - - - +
80J ALA* 1.3 77.9 - - + +
82J TYR* 1.3 73.3 + - + +
84J VAL* 4.3 1.1 - - - +
85J ALA* 3.0 26.1 + - - +
196J ILE* 3.4 32.0 - - + +
200J ALA* 6.0 0.4 - - + -
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Residues in contact with TYR 82 (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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215B GLN* 4.0 5.5 + - - +
219B ARG* 5.7 0.2 + - - -
34J GLY 5.9 0.7 - - - -
39J PRO* 2.9 31.2 - - + -
44J MET* 4.6 15.5 - - - -
47J ALA* 6.2 0.9 - - + -
48J HIS* 3.0 31.6 + + - -
51J VAL* 3.5 32.8 - - + -
52J ALA* 3.6 21.9 - - - +
55J VAL* 3.8 14.3 - - + +
78J GLU* 3.0 50.9 + - + +
79J ARG* 3.9 5.6 - - - +
81J PHE* 1.3 78.4 - - + +
83J ALA* 1.3 69.9 + - - +
85J ALA* 3.5 3.8 - - - +
86J ALA* 3.0 22.1 + - - +
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Residues in contact with ALA 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J GLY 5.6 2.5 - - - -
35J VAL* 5.5 0.7 - - - +
36J GLY* 5.7 6.5 - - - +
79J ARG* 2.9 20.8 + - - +
80J ALA 3.1 2.0 + - - +
82J TYR* 1.3 82.1 - - - +
84J VAL* 1.3 64.7 + - - +
86J ALA* 2.8 12.0 + - - +
87J ILE* 2.9 17.2 + - + +
173J HIS* 2.8 44.0 - - + +
199J LEU* 4.5 2.7 - - + -
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Residues in contact with VAL 84 (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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80J ALA 3.1 10.1 + - - +
81J PHE 4.3 1.3 - - - +
83J ALA* 1.3 75.7 - - - +
85J ALA* 1.3 57.1 + - - +
87J ILE* 3.0 14.0 - - + +
88J MET* 2.5 40.9 + - + +
192J TRP* 5.3 4.5 - - + +
195J LEU* 4.0 20.2 - - + -
196J ILE* 3.7 31.2 - - + -
199J LEU* 4.7 3.2 - - + +
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Residues in contact with ALA 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J LEU* 4.6 9.9 - - + -
17J VAL* 4.5 8.4 - - + +
31J LEU* 4.2 5.3 - - + +
51J VAL* 4.0 27.6 - - + -
81J PHE 3.0 19.6 + - - +
82J TYR* 3.5 3.8 - - - +
84J VAL* 1.3 78.1 - - - +
86J ALA* 1.3 63.1 + - - +
88J MET* 3.7 13.2 - - - +
89J ALA* 3.1 23.8 + - - +
196J ILE* 5.7 1.7 - - - +
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Residues in contact with ALA 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 3.4 28.5 - - + +
32J ARG* 4.2 2.6 - - - -
34J GLY* 3.9 24.2 - - - +
35J VAL* 4.2 5.2 - - + +
44J MET* 6.5 0.2 - - - -
47J ALA* 6.1 2.2 - - + -
82J TYR 3.0 10.7 + - - +
83J ALA 2.8 13.5 + - - +
85J ALA* 1.3 71.0 - - - +
87J ILE* 1.3 64.0 + - - +
89J ALA* 2.9 16.4 + - - +
90J ALA* 2.9 14.7 + - - +
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Residues in contact with ILE 87 (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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35J VAL* 3.7 22.7 - - + +
83J ALA* 2.9 12.7 + - + +
84J VAL* 3.0 37.7 - - + +
86J ALA* 1.3 73.6 - - - +
88J MET* 1.3 62.8 + - + +
90J ALA* 3.1 12.1 + - + +
91J GLN* 3.4 18.6 - - - +
173J HIS 5.9 0.2 - - - +
176J LEU* 3.8 13.9 - - + -
177J PRO* 3.3 39.5 - - + +
180J VAL* 3.3 21.1 - - + -
181J LEU* 4.9 7.6 - - + +
192J TRP* 6.1 1.6 - - + -
195J LEU* 5.7 3.4 - - + -
199J LEU* 6.3 0.2 - - + -
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Residues in contact with MET 88 (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 LEU 5.1 0.7 - - - +
14J VAL* 4.9 7.2 - - + +
17J VAL* 3.6 37.7 - - + -
18J SER* 3.8 22.4 - - - +
21J ILE* 5.9 3.4 - - + -
84J VAL* 2.5 25.9 + - + +
85J ALA* 3.7 5.4 - - - +
87J ILE* 1.3 73.7 - - + +
89J ALA* 1.3 61.5 + - - +
91J GLN* 3.5 19.7 + - - +
96J ARG* 6.0 1.0 - - - +
192J TRP* 3.3 59.9 - - + +
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Residues in contact with ALA 89 (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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17J VAL* 5.1 4.5 - - + -
21J ILE* 5.5 8.9 - - + +
28J ARG* 4.6 7.1 - - - +
31J LEU* 3.4 35.2 - - + -
32J ARG* 4.1 10.5 + - - +
85J ALA 3.1 14.4 + - - +
86J ALA 2.9 10.7 + - - +
88J MET* 1.3 78.0 - - - +
90J ALA* 1.3 56.1 + - - +
91J GLN 3.3 10.3 + - - +
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Residues in contact with ALA 90 (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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32J ARG* 3.8 43.7 + - + +
35J VAL* 4.8 11.2 - - + -
86J ALA 2.9 12.6 + - - +
87J ILE* 3.1 11.1 + - + +
89J ALA* 1.3 76.4 - - - +
91J GLN* 1.3 71.1 + - - +
92J PRO* 3.9 2.9 - - - +
181J LEU* 4.7 9.2 - - + +
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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
------------------------------------------------------------
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