Contacts of the helix formed by residues 12 - 25 (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 GLY 12 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9J HIS 5.7 1.6 - - - -
10J MET 3.4 4.0 + - - -
11J ILE* 1.3 74.9 - - - +
13J SER* 1.3 67.7 + - - -
14J GLY 3.1 3.1 - - - -
15J HIS* 3.0 31.8 + - - +
16J LEU* 3.5 7.8 + - - +
125J LYS* 4.4 4.9 - - - -
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Residues in contact with SER 13 (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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93E LYS* 3.4 30.1 + - - -
95E TYR* 4.0 24.3 - - - +
12J GLY* 1.3 70.3 - - - -
14J GLY* 1.3 62.8 + - - +
16J LEU* 3.2 11.2 + - - +
17J GLN* 3.0 41.6 + - - +
125J LYS* 4.4 10.0 + - - +
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Residues in contact with GLY 14 (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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12J GLY 3.1 1.4 - - - -
13J SER* 1.3 79.3 - - - +
15J HIS* 1.3 57.1 + - - +
17J GLN* 3.3 12.6 + - - +
18J SER* 3.0 29.5 + - - -
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Residues in contact with HIS 15 (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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10J MET 4.0 16.2 - - - -
11J ILE* 4.4 6.5 - - + -
12J GLY* 3.0 27.1 + - - +
14J GLY* 1.3 76.3 + - - +
16J LEU* 1.3 63.3 + - + +
18J SER* 2.7 21.5 + - - -
19J LEU* 3.2 12.8 + - - +
79J GLN* 4.5 21.7 + - + +
80J LEU* 4.0 21.2 - - + +
83J LEU* 3.6 40.4 - - + +
86J ARG* 4.7 8.7 + - - -
121J PHE* 6.1 0.2 - - + -
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Residues in contact with LEU 16 (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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95E TYR* 3.9 27.6 - - + +
11J ILE* 4.1 19.5 - - + -
12J GLY 3.8 9.9 - - - +
13J SER* 3.2 6.6 + - - +
15J HIS* 1.3 76.7 - - + +
17J GLN* 1.3 60.5 + - - +
19J LEU* 3.2 8.5 + - + +
20J GLN* 2.8 29.5 + - - +
118J LYS* 5.2 6.9 - - + +
121J PHE* 4.3 9.9 - - + +
122J ASN* 3.7 44.4 - - + +
125J LYS* 3.5 29.4 - - + +
126J ASN* 5.9 0.2 - - - +
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Residues in contact with GLN 17 (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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93E LYS* 5.3 6.3 - - - +
94E ASP 4.5 12.5 + - - -
95E TYR* 4.9 13.3 + - + +
99E ASP* 5.4 15.2 - - + +
13J SER* 3.0 37.0 + - - +
14J GLY* 3.7 9.3 - - - +
16J LEU* 1.3 72.9 - - - +
18J SER* 1.3 56.6 + - - +
19J LEU 3.0 1.6 - - - -
20J GLN* 4.4 5.2 - - - +
21J ARG* 2.7 49.7 + - + +
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Residues in contact with SER 18 (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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14J GLY 3.0 13.3 + - - -
15J HIS* 2.7 26.2 + - - -
17J GLN* 1.3 76.0 - - - +
19J LEU* 1.3 55.5 + - - +
21J ARG* 3.6 19.3 + - - +
22J LEU* 3.1 25.3 + - - +
73J ASN* 4.9 0.5 - - - +
76J ALA* 3.8 31.4 + - - +
79J GLN* 4.9 9.7 + - - +
80J LEU* 4.6 8.1 - - - +
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Residues in contact with LEU 19 (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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15J HIS 3.2 15.3 + - - +
16J LEU* 3.5 9.2 - - + +
17J GLN 3.0 0.6 - - - -
18J SER* 1.3 79.3 - - - +
20J GLN* 1.3 62.5 + - - +
22J LEU* 3.5 10.8 - - + +
23J ILE* 3.3 24.5 + - + +
65J MET* 4.5 12.1 - - + -
80J LEU* 4.0 23.3 - - + -
114J LEU* 5.1 3.1 - - + +
117J VAL* 4.0 13.5 - - + +
118J LYS* 3.5 38.6 - - + +
121J PHE* 3.6 33.4 - - + -
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Residues in contact with GLN 20 (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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99E ASP* 5.2 14.8 - - + +
68I ARG* 5.0 5.7 - - - +
16J LEU 2.8 17.2 + - - +
17J GLN* 3.9 5.4 - - - +
19J LEU* 1.3 73.7 - - - +
21J ARG* 1.3 55.3 + - + +
22J LEU 3.0 1.3 - - - -
23J ILE* 2.7 39.4 + - - +
24J ASP* 2.8 51.7 + - - +
118J LYS* 3.0 36.9 + - + +
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Residues in contact with ARG 21 (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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99E ASP* 3.6 28.5 - - + +
17J GLN* 2.7 32.0 + - - +
18J SER* 3.6 25.2 + - - +
20J GLN* 1.3 72.9 - - - +
22J LEU* 1.3 60.4 + - - +
24J ASP* 4.0 10.0 - - - +
25J SER* 3.2 24.4 + - - -
72J PRO* 3.7 34.4 + - - +
73J ASN* 4.4 8.9 + - - +
76J ALA* 5.3 0.8 - - - +
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Residues in contact with LEU 22 (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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18J SER 3.1 20.1 + - - +
19J LEU* 3.5 13.9 - - + +
20J GLN 3.0 0.2 - - - -
21J ARG* 1.3 81.4 - - - +
23J ILE* 1.3 57.2 + - - +
25J SER* 3.1 4.3 + - - -
26J GLN* 2.9 30.0 + - - +
65J MET* 4.4 3.4 - - + -
67J PHE* 3.6 26.2 - - + -
73J ASN* 3.5 25.5 + - + +
76J ALA* 4.6 3.4 - - + -
77J ILE* 3.5 32.8 - - + -
80J LEU* 5.6 0.7 - - + -
114J LEU* 3.4 38.1 - - + -
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Residues in contact with ILE 23 (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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68I ARG* 3.7 24.6 + - - +
19J LEU* 3.3 15.7 + - + +
20J GLN* 2.7 24.6 + - - +
22J LEU* 1.3 70.7 - - + +
24J ASP* 1.3 65.8 + - - +
25J SER 3.1 2.7 - - - -
26J GLN* 3.0 25.4 + - - +
111J LEU* 4.1 14.8 - - + +
114J LEU* 3.6 23.8 - - + -
115J GLU* 4.0 30.5 - - + +
118J LYS* 3.9 31.9 - - + +
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Residues in contact with ASP 24 (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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99E ASP* 4.9 9.0 - - - +
100E LYS* 5.7 4.5 + - - +
67I PHE* 5.1 1.2 - - - -
68I ARG* 3.4 34.5 + - - +
71I THR* 3.7 36.8 + - + +
72I PRO* 5.6 2.7 - - + -
73I ASN* 4.7 0.5 + - - -
20J GLN* 2.8 54.3 + - - +
21J ARG* 3.5 9.0 + - - +
23J ILE* 1.3 72.4 - - - +
25J SER* 1.3 60.8 + - - +
26J GLN 3.5 5.0 + - - +
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Residues in contact with SER 25 (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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25I SER* 3.7 13.6 - - - -
26I GLN* 2.9 15.2 + - - -
67I PHE* 3.7 1.6 - - - -
71I THR* 5.4 1.1 - - - -
72I PRO* 6.3 2.2 - - - -
73I ASN* 2.6 36.1 + - - +
21J ARG 3.2 11.6 + - - -
22J LEU 3.1 15.9 + - - -
24J ASP* 1.3 78.2 - - - +
26J GLN* 1.3 63.6 + - - +
27J MET 3.5 0.2 + - - -
73J ASN* 3.3 17.5 + - - -
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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