Contacts of the helix formed by residues 71 - 88 (chain J) in PDB entry 3UF2
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 THR 71 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ASP* 3.7 36.5 + - + -
25I SER* 5.9 0.4 - - - -
67J PHE* 3.8 9.2 - - - +
68J ARG* 2.8 35.6 + - + +
69J ASP 3.7 7.0 - - - +
70J ASN* 1.3 81.0 - - - +
72J PRO* 1.3 75.7 - - + +
73J ASN* 3.9 2.8 + - - +
74J ALA* 2.8 23.7 + - - +
75J ILE* 2.9 12.0 + - - +
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Residues in contact with PRO 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ASP* 5.7 3.1 - - + -
21J ARG* 3.7 26.8 + - - +
70J ASN 4.4 1.8 - - - +
71J THR* 1.3 87.8 - - + +
73J ASN* 1.3 60.2 + - - +
75J ILE* 3.6 11.3 + - + +
76J ALA* 3.0 26.0 + - - +
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Residues in contact with ASN 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I SER* 3.2 38.7 + - - +
18J SER 4.9 1.6 - - - +
21J ARG* 4.4 8.3 + - - +
22J LEU* 3.5 28.0 + - + +
25J SER* 3.3 16.5 + - - -
26J GLN* 3.9 4.0 - - - +
67J PHE* 3.8 24.2 - - + -
71J THR* 3.1 3.7 + - - +
72J PRO* 1.3 80.6 - - - +
74J ALA* 1.3 68.1 + - - +
76J ALA* 3.0 7.5 + - - +
77J ILE* 3.0 26.0 + - - +
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Residues in contact with ALA 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ARG* 5.7 0.5 + - - -
67J PHE* 3.8 21.4 - - + +
68J ARG 3.2 28.3 - - - +
69J ASP* 4.3 1.6 - - - -
70J ASN 3.9 8.1 - - - +
71J THR* 2.8 18.4 + - - +
73J ASN* 1.3 76.0 - - - +
75J ILE* 1.3 61.4 + - - +
77J ILE* 3.2 13.4 + - - +
78J VAL* 3.3 17.5 + - - +
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Residues in contact with ILE 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J ASN* 3.7 35.2 - - + +
71J THR 2.9 17.3 + - - +
72J PRO* 3.8 8.7 - - + +
74J ALA* 1.3 72.1 - - - +
76J ALA* 1.3 67.0 + - - +
78J VAL* 3.2 11.4 + - + +
79J GLN* 3.1 40.5 + - + +
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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
----------------------------------------------------------
18J SER* 3.8 37.5 + - - +
21J ARG* 5.3 2.2 - - - +
22J LEU* 4.6 4.7 - - + -
72J PRO 3.0 16.7 + - - +
73J ASN* 3.0 13.7 + - - +
75J ILE* 1.3 76.5 - - - +
77J ILE* 1.3 63.1 + - - +
79J GLN* 3.2 15.0 + - - +
80J LEU* 3.0 28.6 + - + +
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Residues in contact with ILE 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU* 3.5 16.2 - - + -
61J MET* 4.0 12.8 - - + +
65J MET* 3.4 53.2 - - + +
66J ARG* 3.8 16.4 - - - +
67J PHE* 3.8 11.0 - - + -
73J ASN 3.0 18.7 + - - +
74J ALA* 3.5 8.3 - - - +
76J ALA* 1.3 75.6 - - - +
78J VAL* 1.3 62.7 + - - +
80J LEU* 3.3 13.2 + - + +
81J GLN* 2.9 40.5 + - - +
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Residues in contact with VAL 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ARG* 5.6 3.8 - - - +
74J ALA 3.3 13.4 + - - +
75J ILE* 3.2 14.2 + - + +
77J ILE* 1.3 78.0 - - + +
79J GLN* 1.3 58.6 + - + +
81J GLN* 2.9 18.2 + - + +
82J GLU* 2.8 50.7 + - + +
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Residues in contact with GLN 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J HIS* 4.5 17.7 + - + +
18J SER* 4.9 10.3 + - - +
75J ILE* 3.1 28.3 + - + +
76J ALA* 3.5 12.8 - - - +
78J VAL* 1.3 77.3 - - + +
80J LEU* 1.3 58.4 + - + +
82J GLU* 3.1 19.4 + - - +
83J LEU* 2.8 30.5 + - - +
86J ARG* 5.3 1.0 + - - -
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Residues in contact with LEU 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J HIS* 4.0 37.5 - - + +
18J SER* 4.6 5.4 - - - +
19J LEU* 4.0 33.9 - - + -
22J LEU* 5.6 0.2 - - + -
61J MET* 3.7 21.1 - - - -
65J MET* 5.3 0.7 - - + -
76J ALA* 3.0 19.7 + - + +
77J ILE* 3.3 19.9 + - + +
79J GLN* 1.3 75.6 - - - +
81J GLN* 1.3 52.8 + - - +
83J LEU* 3.5 6.3 + - + +
84J SER* 2.5 37.3 + - - -
121J PHE* 4.3 27.1 - - + -
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Residues in contact with GLN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN* 4.8 4.6 + - - +
61J MET* 4.0 18.8 - - + +
62J GLU* 3.5 41.8 + - - +
66J ARG* 3.6 17.4 + - - +
77J ILE* 2.9 26.1 + - - +
78J VAL* 2.9 17.9 + - + +
80J LEU* 1.3 74.8 - - - +
82J GLU* 1.3 64.8 + - - +
84J SER* 3.5 9.0 + - - -
85J LEU* 3.3 26.7 + - - +
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Residues in contact with GLU 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J VAL* 2.8 37.8 + - + +
79J GLN* 3.1 18.0 + - - +
81J GLN* 1.3 74.8 - - + +
83J LEU* 1.3 65.5 + - - +
85J LEU* 3.1 21.2 + - + +
86J ARG* 3.2 37.0 + - - +
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Residues in contact with LEU 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J MET* 3.5 43.3 - - + +
11J ILE* 4.1 21.3 - - + -
15J HIS* 3.6 34.8 - - + +
79J GLN 2.8 16.1 + - - +
80J LEU* 3.6 5.2 - - + +
82J GLU* 1.3 75.5 - - - +
84J SER* 1.3 53.3 + - - +
86J ARG* 3.0 26.7 + - - +
87J LEU* 2.8 40.1 + - + +
121J PHE* 4.2 18.4 - - + -
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Residues in contact with SER 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J PHE* 3.6 9.5 - - - -
58J GLN* 3.1 38.7 + - - -
61J MET* 3.6 6.2 - - - +
80J LEU 2.5 24.8 + - - -
81J GLN* 3.6 6.3 - - - -
82J GLU 3.2 0.2 - - - -
83J LEU* 1.3 77.2 - - - +
85J LEU* 1.3 61.8 + - - +
87J LEU* 3.1 12.6 + - - +
88J LYS* 3.0 25.3 + - - +
121J PHE* 3.8 11.6 - - - -
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Residues in contact with LEU 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLN* 4.9 8.3 - - - +
81J GLN 3.3 13.6 + - - +
82J GLU* 3.1 15.7 + - + +
84J SER* 1.3 79.5 - - - +
86J ARG* 1.3 63.3 + - + +
88J LYS* 3.4 42.2 + - + +
89J SER* 4.4 1.6 + - - -
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Residues in contact with ARG 86 (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 TYR* 6.3 0.2 - - + -
10J MET* 3.6 32.6 + - + +
15J HIS* 4.7 8.5 + - - -
79J GLN 5.3 0.8 + - - -
82J GLU* 3.4 32.9 + - - +
83J LEU* 3.0 42.7 + - - +
85J LEU* 1.3 78.7 - - + +
87J LEU* 1.3 57.6 + - - +
88J LYS 3.4 0.2 + - - -
89J SER* 2.6 28.8 + - - -
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Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J MET* 3.8 28.0 - - + -
11J ILE* 3.8 32.5 - - + -
54J PHE* 3.4 35.4 - - + -
83J LEU* 2.8 31.8 + - + +
84J SER* 3.1 5.1 + - - +
86J ARG* 1.3 73.8 - - - +
88J LYS* 1.3 55.7 + - - +
89J SER 2.9 3.1 - - - -
90J CYS* 2.7 31.0 + - - +
91J PHE* 3.4 19.1 - - + -
121J PHE* 4.4 5.6 - - + -
124J THR* 4.9 3.1 - - + -
128J LEU* 4.3 14.4 - - + -
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Residues in contact with LYS 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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54J PHE* 4.5 14.4 - - + -
55J LEU* 6.3 2.9 - - + -
58J GLN* 5.1 6.5 - - - +
84J SER 3.0 18.7 + - - +
85J LEU* 3.4 33.2 - - + +
86J ARG 3.3 0.4 - - - -
87J LEU* 1.3 75.0 - - - +
89J SER* 1.3 53.3 + - - +
91J PHE* 2.8 31.2 + - - +
93J LYS* 4.4 23.9 + - - +
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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
------------------------------------------------------------
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