Contacts of the helix formed by residues 12 - 25 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I HIS 5.8 0.7 - - - -
10I MET 3.3 7.4 + - - -
11I ILE* 1.3 75.0 - - - +
13I SER* 1.3 67.7 + - - -
14I GLY* 2.9 3.6 - - - -
15I HIS* 2.8 31.4 + - - +
16I LEU* 3.5 7.4 + - - +
125I LYS* 4.6 1.1 - - - -
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Residues in contact with SER 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE 4.2 0.4 + - - -
12I GLY* 1.3 70.5 - - - -
14I GLY* 1.3 52.7 + - - +
16I LEU* 3.0 15.0 + - - +
17I GLN* 2.8 52.5 + - - +
125I LYS* 4.4 14.2 + - - +
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Residues in contact with GLY 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I GLY* 2.9 2.6 + - - -
13I SER* 1.3 78.6 - - - +
15I HIS* 1.3 61.0 + - - +
17I GLN* 3.5 7.7 + - - +
18I SER* 3.2 22.9 + - - -
79I GLN* 5.1 2.7 - - - +
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Residues in contact with HIS 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I MET 4.0 15.5 - - - -
11I ILE* 4.4 5.6 - - + -
12I GLY* 2.8 27.9 + - - +
14I GLY* 1.3 76.7 - - - +
16I LEU* 1.3 63.1 + - + +
18I SER* 2.7 21.3 + - - -
19I LEU* 3.3 10.4 + - - +
79I GLN* 4.0 35.8 + - + +
80I LEU* 4.1 16.4 - - + +
83I LEU* 3.9 30.0 - - + +
86I ARG* 4.1 21.0 + - - -
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Residues in contact with LEU 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ILE* 3.7 20.9 - - + -
12I GLY 3.9 8.5 - - - +
13I SER* 3.0 12.0 + - - +
15I HIS* 1.3 76.1 - - + +
17I GLN* 1.3 66.2 + - + +
19I LEU* 3.2 12.1 + - + +
20I GLN* 3.2 21.0 + - - +
118I LYS* 5.9 1.6 - - - +
121I PHE* 3.9 23.3 - - + +
122I ASN* 3.4 28.9 - - - +
125I LYS* 3.4 34.1 - - + +
126I ASN* 5.9 0.9 - - - +
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Residues in contact with GLN 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I SER* 2.8 32.8 + - - +
14I GLY* 3.9 7.2 - - - +
16I LEU* 1.3 78.5 - - + +
18I SER* 1.3 56.9 + - - +
20I GLN* 3.3 6.4 + - - +
21I ARG* 2.8 66.6 + - - +
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Residues in contact with SER 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I GLY 3.2 12.6 + - - -
15I HIS* 2.7 25.3 + - - -
17I GLN* 1.3 78.2 - - - +
19I LEU* 1.3 56.8 + - - +
21I ARG* 3.9 13.6 - - - +
22I LEU* 2.9 28.6 + - - +
73I ASN* 5.2 0.3 - - - +
76I ALA* 4.0 28.6 + - - +
79I GLN* 4.3 9.6 + - - -
80I LEU* 5.0 2.8 - - - +
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I HIS 3.3 6.0 + - - +
16I LEU* 3.2 15.2 + - + +
17I GLN 3.1 0.4 - - - -
18I SER* 1.3 78.7 + - - +
20I GLN* 1.3 60.1 + - - +
22I LEU* 3.2 13.9 + - + +
23I ILE* 2.9 34.7 + - + +
65I MET* 4.9 10.8 - - + -
80I LEU* 3.7 34.8 - - + -
114I LEU* 5.4 3.1 - - + +
117I VAL* 4.5 15.5 - - + +
118I LYS* 4.3 24.7 - - + +
121I PHE* 3.8 37.5 - - + -
122I ASN* 6.1 0.2 - - - +
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Residues in contact with GLN 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I LEU 3.2 9.7 + - - +
17I GLN* 3.7 7.9 - - - +
19I LEU* 1.3 76.2 - - - +
21I ARG* 1.3 57.2 + - + +
23I ILE* 3.0 21.8 + - - +
24I ASP* 2.7 56.4 + - - +
115I GLU* 5.7 0.6 + - - -
118I LYS* 3.1 32.9 + - + +
68J ARG* 3.1 30.2 - - - +
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Residues in contact with ARG 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLN* 2.8 55.0 + - - +
18I SER* 3.9 11.2 - - - +
20I GLN* 1.3 76.9 - - + +
22I LEU* 1.3 61.4 + - - +
24I ASP* 3.6 12.0 + - - +
25I SER* 3.3 22.5 + - - -
73I ASN* 4.6 3.3 - - - +
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Residues in contact with LEU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I SER 2.9 18.6 + - - +
19I LEU* 3.2 15.0 - - + +
21I ARG* 1.3 75.4 - - - +
23I ILE* 1.3 65.0 + - + +
25I SER* 2.6 22.0 + - - -
26I GLN* 3.3 15.9 + - - +
65I MET* 4.6 1.6 - - + -
67I PHE* 3.5 26.7 - - + -
73I ASN* 3.7 24.2 + - + +
76I ALA* 4.6 5.4 - - + -
77I ILE* 3.5 33.2 - - + -
80I LEU* 5.5 0.4 - - + -
114I LEU* 3.5 36.3 - - + -
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Residues in contact with ILE 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 2.9 21.4 + - + +
20I GLN* 3.4 12.3 - - - +
22I LEU* 1.3 78.8 - - + +
24I ASP* 1.3 65.9 + - - +
26I GLN* 3.1 23.7 + - - +
111I LEU* 4.1 17.8 - - + +
114I LEU* 3.7 43.5 - - + +
115I GLU* 4.4 10.5 - - - +
118I LYS* 3.8 31.0 - - + -
68J ARG* 3.4 27.3 + - - +
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Residues in contact with ASP 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLN* 2.7 45.5 + - - +
21I ARG* 3.6 12.1 - - - +
23I ILE* 1.3 73.1 - - - +
25I SER* 1.3 60.8 + - - +
26I GLN 3.4 6.6 + - - +
67J PHE* 4.4 4.7 - - - -
68J ARG* 3.1 43.3 + - - +
71J THR* 3.7 40.2 + - + +
72J PRO* 5.7 2.7 - - + -
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Residues in contact with SER 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ARG 3.3 11.8 + - - -
22I LEU 2.6 21.8 + - - -
24I ASP* 1.3 77.9 - - - +
26I GLN* 1.3 64.5 + - - +
73I ASN* 3.5 11.9 + - - -
25J SER* 3.7 14.1 - - - -
26J GLN* 2.7 32.1 + - - -
67J PHE* 3.4 2.7 - - - -
71J THR* 5.7 0.4 - - - -
73J ASN* 3.2 24.0 + - - +
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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