Contacts of the helix formed by residues 12 - 26 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B HIS 5.7 1.6 - - - -
10B MET 3.5 3.8 + - - -
11B ILE* 1.3 75.1 - - - +
13B SER* 1.3 67.0 + - - -
14B GLY 3.0 5.0 + - - -
15B HIS* 3.1 30.8 + - - +
16B LEU* 3.6 7.4 + - - +
125B LYS* 4.1 4.0 - - - -
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Residues in contact with SER 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY* 1.3 72.3 - - - -
14B GLY* 1.3 62.4 + - - +
16B LEU* 3.0 15.4 + - - +
17B GLN* 2.9 44.1 + - - +
125B LYS* 4.0 15.7 + - - +
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 3.0 3.0 - - - -
13B SER* 1.3 79.0 - - - +
15B HIS* 1.3 56.9 + - - +
17B GLN* 3.2 12.5 + - - +
18B SER* 3.0 30.0 + - - -
79B GLN* 6.1 0.7 - - - -
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MET 4.1 8.7 - - - -
11B ILE* 4.4 9.9 - - + -
12B GLY* 3.1 32.1 + - - +
14B GLY* 1.3 75.8 + - - +
16B LEU* 1.3 63.9 + - + +
18B SER* 3.0 19.5 + - - -
19B LEU* 3.1 17.9 + - + +
79B GLN* 4.7 18.0 + - + +
80B LEU* 4.0 24.6 - - + +
83B LEU* 3.6 38.2 - - + +
121B PHE* 6.1 0.4 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.5 8.3 - - + -
12B GLY 4.0 9.6 - - - +
13B SER* 3.0 12.7 + - - +
15B HIS* 1.3 78.2 - - + +
17B GLN* 1.3 59.3 + - + +
19B LEU* 3.5 10.2 + - + +
20B GLN* 3.0 26.7 + - - +
118B LYS* 5.1 4.9 - - + +
121B PHE* 4.3 15.9 - - + +
122B ASN* 3.2 49.6 - - - +
125B LYS* 3.7 26.9 - - + +
126B ASN* 6.0 0.4 - - - +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 2.9 35.0 + - - +
14B GLY* 3.8 11.0 - - - +
15B HIS 3.2 0.2 - - - -
16B LEU* 1.3 79.1 - - + +
18B SER* 1.3 59.8 + - - +
19B LEU 3.2 0.4 - - - -
20B GLN* 3.9 5.9 - - - +
21B ARG* 3.0 39.4 + - + +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.0 13.1 + - - -
15B HIS* 3.0 18.7 + - - -
17B GLN* 1.3 74.4 - - - +
19B LEU* 1.3 64.0 + - - +
21B ARG* 4.0 8.9 - - - +
22B LEU* 3.2 22.7 + - - +
73B ASN* 4.9 0.9 - - - +
76B ALA* 4.1 28.7 + - - +
79B GLN* 4.2 14.0 + - - -
80B LEU* 5.1 4.0 - - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 3.1 20.6 + - + +
16B LEU* 3.5 10.5 - - + +
18B SER* 1.3 75.1 + - - +
20B GLN* 1.3 55.3 + - - +
22B LEU* 3.0 9.9 + - + +
23B ILE* 2.8 44.4 + - + +
65B MET* 4.9 10.8 - - + -
77B ILE* 5.6 1.1 - - + -
80B LEU* 3.7 28.9 - - + -
114B LEU* 5.4 4.3 - - + +
117B VAL* 4.5 15.5 - - + -
118B LYS* 4.2 24.9 - - + +
121B PHE* 3.7 36.8 - - + -
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 5.5 1.6 - - - +
16B LEU 3.0 17.0 + - - +
17B GLN* 3.5 8.3 + - - +
19B LEU* 1.3 76.9 - - - +
21B ARG* 1.3 52.1 + - + +
23B ILE* 3.0 19.9 + - - +
24B ASP* 2.7 70.1 + - - +
115B GLU* 5.1 0.6 + - - -
118B LYS* 3.1 35.7 + - - +
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 5.0 14.5 - - - +
17B GLN* 3.0 28.2 + - + +
18B SER* 4.0 7.4 - - - +
20B GLN* 1.3 75.5 - - - +
22B LEU* 1.3 57.1 + - - +
24B ASP* 3.2 10.6 + - - +
25B SER* 2.9 30.4 + - - -
72B PRO* 4.8 16.6 - - - +
73B ASN* 4.6 2.7 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B SER 3.2 11.4 + - - +
19B LEU* 3.0 16.9 + - + +
21B ARG* 1.3 77.2 - - - +
23B ILE* 1.3 62.5 + - + +
25B SER* 2.6 18.3 + - - -
26B GLN* 3.2 15.5 - - - +
65B MET* 4.8 1.1 - - + -
67B PHE* 3.8 19.5 - - + -
73B ASN* 3.4 48.2 + - + +
76B ALA* 4.6 5.6 - - + -
77B ILE* 3.8 27.8 - - + -
114B LEU* 3.6 35.0 - - + -
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 2.8 27.8 + - + +
20B GLN* 3.4 19.7 - - - +
22B LEU* 1.3 75.6 - - + +
24B ASP* 1.3 63.4 + - - +
25B SER 3.4 0.3 + - - -
26B GLN 3.6 8.7 + - - +
111B LEU* 3.7 27.6 - - + +
114B LEU* 3.9 33.9 - - + +
115B GLU* 4.3 20.4 - - - +
118B LYS* 3.6 43.3 - - + -
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 5.0 2.1 - - - -
68A ARG* 3.4 38.9 + - - +
71A THR* 3.5 38.2 + - + +
72A PRO* 6.4 0.2 - - + -
20B GLN* 2.7 56.1 + - - +
21B ARG* 3.2 10.0 + - - +
23B ILE* 1.3 75.8 - - - +
25B SER* 1.3 59.6 + - - +
26B GLN 4.4 3.5 - - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 4.5 7.0 - - - -
26A GLN* 2.8 21.6 + - - -
67A PHE* 3.6 2.9 - - - -
71A THR* 5.6 0.7 - - - -
72A PRO* 6.4 1.3 - - - -
73A ASN* 2.9 24.4 + - - +
21B ARG 2.9 11.0 + - - -
22B LEU* 2.6 22.4 + - - -
24B ASP* 1.3 78.5 - - - +
26B GLN* 1.3 63.9 + - - +
73B ASN* 3.1 25.8 + - - -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER 2.8 27.2 + - - -
26A GLN* 3.6 5.7 - - - +
27A MET* 2.8 32.4 + - - +
67A PHE* 3.9 7.4 - - - -
68A ARG 5.3 0.7 + - - -
22B LEU* 3.2 13.4 + - - +
23B ILE 3.6 11.4 + - - +
24B ASP 3.5 3.8 - - - +
25B SER* 1.3 95.4 + - - +
27B MET* 1.3 66.2 + - - +
28B GLU* 3.7 7.8 + - - +
67B PHE* 3.4 17.4 - - - -
73B ASN* 3.5 2.4 - - - +
110B PRO* 5.7 6.4 - - + +
111B LEU* 4.1 15.4 - - + +
114B LEU* 3.8 21.8 - - + -
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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