Contacts of the helix formed by residues 12 - 25 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D HIS* 4.6 4.2 + - - -
10D MET 3.5 3.6 + - - -
11D ILE* 1.3 76.7 - - - +
13D SER* 1.3 65.3 + - - -
14D GLY 3.1 3.1 - - - -
15D HIS* 3.2 27.4 + - - +
16D LEU* 3.6 13.5 + - - +
125D LYS* 4.1 5.2 - - - -
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Residues in contact with SER 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 4.5 2.6 + - - -
143B PHE 5.4 0.7 + - - -
144B ALA* 5.0 17.1 - - - -
12D GLY* 1.3 70.0 - - - -
14D GLY* 1.3 56.7 + - - +
16D LEU* 3.1 14.9 + - - +
17D GLN* 2.7 62.7 + - - +
125D LYS* 4.2 7.6 - - - +
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Residues in contact with GLY 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP* 4.4 11.2 - - - +
12D GLY* 3.1 2.4 - - - -
13D SER* 1.3 82.5 + - - +
15D HIS* 1.3 60.7 + - - +
17D GLN* 3.6 10.9 - - - +
18D SER* 3.2 24.6 + - - -
79D GLN* 5.6 0.5 - - - +
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Residues in contact with HIS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D MET 3.8 15.7 - - - -
11D ILE* 4.6 4.9 - - + -
12D GLY* 3.2 27.9 + - - +
13D SER 3.2 0.6 - - - -
14D GLY* 1.3 76.2 + - - +
16D LEU* 1.3 63.2 + - + +
18D SER* 3.0 19.8 + - - -
19D LEU* 3.2 13.0 + - - +
79D GLN* 4.6 19.3 + - + +
80D LEU* 3.8 24.1 - - + +
83D LEU* 3.7 35.4 - - + +
121D PHE* 6.2 0.7 - - + -
32E GLN* 3.5 27.4 + - - -
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 4.2 9.9 - - + -
12D GLY 3.6 9.6 - - - +
13D SER* 3.1 12.7 + - - +
15D HIS* 1.3 78.1 - - + +
17D GLN* 1.3 60.7 + - + +
19D LEU* 3.2 9.3 + - + +
20D GLN* 2.8 29.3 + - - +
80D LEU* 6.5 0.2 - - + -
118D LYS* 4.8 8.9 - - + +
121D PHE* 3.9 29.4 - - + -
122D ASN* 3.4 35.2 - - + +
125D LYS* 3.9 24.0 - - + +
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Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 2.6 31.6 - - - +
100B LYS* 4.8 4.3 - - + +
101B ALA* 3.1 39.9 - - + +
143B PHE 3.9 8.1 + - - -
144B ALA 5.2 1.6 + - - -
146B CYS 4.2 13.2 + - - +
13D SER* 2.7 47.9 + - - +
14D GLY 3.5 3.9 + - - +
15D HIS 3.3 0.2 - - - -
16D LEU* 1.3 72.8 - - + +
18D SER* 1.3 60.0 - - - +
20D GLN* 3.3 7.1 + - + +
21D ARG* 2.9 27.8 + - - +
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLY 3.2 13.9 + - - -
15D HIS* 3.0 17.3 + - - -
17D GLN* 1.3 73.8 - - - +
19D LEU* 1.3 60.5 + - - +
21D ARG* 3.5 12.4 - - - +
22D LEU* 2.9 28.1 + - - +
73D ASN* 4.9 0.7 - - - +
76D ALA* 4.2 26.9 + - - +
79D GLN* 4.4 12.8 + - - -
80D LEU* 5.1 3.3 - - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D HIS 3.2 11.1 + - - +
16D LEU* 3.4 12.6 - - + +
17D GLN 3.2 0.2 - - - -
18D SER* 1.3 79.6 + - - +
20D GLN* 1.3 63.4 + - - +
22D LEU* 3.2 10.5 + - + +
23D ILE* 3.1 27.2 + - + +
65D MET* 5.5 8.1 - - + -
76D ALA* 6.0 0.2 - - - -
80D LEU* 4.4 22.0 - - + -
114D LEU* 4.0 7.6 - - + +
117D VAL* 4.5 7.0 - - + -
118D LYS* 3.5 46.4 - - + +
121D PHE* 3.8 28.7 - - + -
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 4.5 8.7 - - - +
16D LEU 2.8 16.3 + - - +
17D GLN* 3.5 8.7 - - + +
19D LEU* 1.3 74.7 - - - +
21D ARG* 1.3 60.4 + - - +
23D ILE* 3.1 19.3 + - - +
24D ASP* 2.9 61.2 + - - +
115D GLU* 4.7 2.8 + - - -
118D LYS* 3.2 36.6 + - + +
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS* 3.4 36.7 - - + +
21C ARG* 6.4 0.2 - - - +
17D GLN 2.9 17.4 + - - +
18D SER* 3.5 12.8 - - - +
20D GLN* 1.3 75.2 - - - +
22D LEU* 1.3 62.8 + - - +
24D ASP* 3.2 20.3 + - + +
25D SER* 3.3 17.4 + - - +
72D PRO* 3.5 40.4 + - - +
73D ASN* 4.5 8.6 + - - +
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D SER 2.9 12.6 + - - +
19D LEU* 3.3 17.3 - - + +
21D ARG* 1.3 78.8 - - - +
23D ILE* 1.3 61.8 + - + +
25D SER* 3.3 3.5 + - - -
26D GLN* 3.1 28.5 + - - +
65D MET* 4.4 3.4 - - + -
67D PHE* 3.6 29.6 - - + -
73D ASN* 3.5 25.6 - - + +
76D ALA* 4.6 6.1 - - + -
77D ILE* 3.5 34.1 - - + -
80D LEU* 5.7 1.3 - - + -
114D LEU* 3.5 37.7 - - + -
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Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ARG* 3.8 24.0 + - - +
19D LEU* 3.1 17.9 + - + +
20D GLN* 3.1 13.1 + - - +
22D LEU* 1.3 76.7 - - + +
24D ASP* 1.3 65.5 + - - +
26D GLN* 3.1 19.4 + - - +
111D LEU* 4.7 15.9 - - + +
114D LEU* 3.7 49.8 - - + +
115D GLU* 4.0 18.4 - - + +
118D LYS* 3.9 28.0 - - + -
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C PHE* 4.6 1.6 - - - -
68C ARG* 3.2 39.6 + - - +
71C THR* 4.0 31.0 + - + +
72C PRO* 6.2 0.7 - - + -
20D GLN* 2.9 46.7 + - - +
21D ARG* 3.6 15.9 - - + +
23D ILE* 1.3 77.8 - - - +
25D SER* 1.3 60.8 + - - +
26D GLN 3.3 6.8 + - - +
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Residues in contact with SER 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C SER* 3.9 11.4 - - - -
26C GLN* 2.8 22.7 + - - -
67C PHE* 3.4 3.0 - - - -
71C THR* 5.5 1.8 - - - -
73C ASN* 2.8 30.7 + - - +
21D ARG* 3.3 11.0 + - - +
22D LEU 3.3 6.8 + - - -
23D ILE 3.3 0.2 - - - -
24D ASP* 1.3 76.2 - - - +
26D GLN* 1.3 64.2 + - - +
73D ASN* 3.3 26.9 + - - -
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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
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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