Contacts of the helix formed by residues 14 - 26 (chain F) in PDB entry 5W97
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 14 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER 5.0 0.2 - - - +
66C THR 4.0 5.4 - - - +
67C PHE 3.7 6.1 - - - +
69C GLY* 3.4 31.8 - - - +
13F ALA* 1.3 76.2 - - - +
15F GLY* 1.3 77.8 + - - +
16F LEU 3.3 0.2 + - - -
17F GLU* 3.1 7.7 + - - +
18F ARG* 2.8 21.1 + - - +
9J GLN* 3.7 29.0 + - - +
13J GLN* 2.9 28.0 + - - +
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Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLN 3.6 15.3 - - - -
14F THR* 1.3 88.5 + - - +
16F LEU* 1.3 57.7 + - - -
18F ARG* 3.3 3.4 - - - +
19F GLU* 3.1 29.0 + - - +
13J GLN* 4.6 8.5 - - - +
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Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C HIS* 5.8 2.0 - - + -
4C GLN* 3.7 28.5 - - + +
6C HIS 4.2 7.0 - - - +
7C ALA* 4.2 5.6 - - - -
8C TYR 4.9 1.6 - - - +
68C GLN 4.4 0.4 + - - -
69C GLY 3.3 10.2 + - - +
70C HIS* 5.0 15.5 - - + +
72C THR* 3.8 20.2 - - + -
14F THR 3.3 0.2 + - - -
15F GLY* 1.3 70.4 - - - -
17F GLU* 1.3 67.3 + - - +
19F GLU* 3.8 10.5 - - + +
20F VAL* 2.9 32.0 + - + +
31F TYR* 3.4 43.5 - - + +
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Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C SER 4.7 6.2 - - - +
69C GLY* 2.8 19.5 + - - +
71C HIS 3.5 16.3 + - - +
72C THR* 4.0 12.7 - - - +
73C PRO* 5.1 5.8 - - + +
231C HIS* 2.6 40.5 + - - +
303C PGV 4.3 9.1 + - - -
9F ASP* 3.9 17.0 - - - +
13F ALA* 4.1 18.7 - - + +
14F THR 3.1 5.4 + - - +
16F LEU* 1.3 75.9 - - - +
18F ARG* 1.3 61.6 + - - +
20F VAL* 3.5 3.7 + - - +
21F MET* 3.1 23.8 + - + +
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Residues in contact with ARG 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP 3.4 11.7 + - - -
10F GLU* 2.8 32.3 + - - +
11F GLU 4.4 3.9 + - - -
13F ALA* 2.8 36.9 + - - +
14F THR* 2.8 21.2 + - - +
15F GLY 3.3 10.8 - - - +
17F GLU* 1.3 74.9 - - - +
19F GLU* 1.3 67.3 + - + +
21F MET* 2.9 15.5 + - + +
22F LEU* 2.9 55.9 + - + +
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C HIS* 5.4 1.2 + - - -
15F GLY 3.1 17.8 + - - +
16F LEU* 3.3 15.6 + - - +
18F ARG* 1.3 76.1 - - + +
20F VAL* 1.3 62.2 + - - +
22F LEU* 3.4 6.9 + - + +
23F ALA* 3.1 26.6 + - - +
30F PRO* 5.3 0.3 - - - +
31F TYR* 2.6 38.9 + - + -
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ALA* 4.5 0.7 - - + -
72C THR* 4.0 16.4 - - + -
73C PRO* 4.3 17.7 - - + -
16F LEU* 2.9 21.9 + - + +
17F GLU 3.8 4.7 - - - +
19F GLU* 1.3 75.8 - - - +
21F MET* 1.3 61.5 + - - +
23F ALA* 3.6 4.9 + - - +
24F ALA* 3.2 26.4 + - + +
30F PRO* 5.9 0.2 - - - -
31F TYR* 4.0 26.7 - - + -
33F ILE* 3.4 33.4 - - + -
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Residues in contact with MET 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP* 3.8 43.5 - - - +
10F GLU* 4.1 12.1 - - + +
13F ALA* 4.1 8.3 - - + -
17F GLU* 3.1 14.7 + - + +
18F ARG* 2.9 25.4 + - + +
20F VAL* 1.3 75.1 - - - +
22F LEU* 1.3 80.9 + - + +
24F ALA* 3.5 5.9 + - - +
25F ARG* 3.5 43.5 + - - +
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Residues in contact with LEU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 2.9 47.5 + - + +
19F GLU* 4.0 6.7 - - + +
21F MET* 1.3 90.9 - - + +
23F ALA* 1.3 65.6 - - - +
25F ARG* 3.3 35.0 + - - +
26F LYS* 3.6 28.3 + - - +
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Residues in contact with ALA 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F GLU 3.1 17.7 + - - +
20F VAL* 4.0 4.0 - - - +
22F LEU* 1.3 77.3 - - - +
24F ALA* 1.3 60.5 + - - +
26F LYS* 3.2 13.9 + - - +
28F GLN* 2.8 37.6 + - + +
30F PRO* 3.6 35.9 - - + -
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F VAL* 3.2 21.9 + - + +
21F MET* 3.9 6.3 - - - +
22F LEU 3.2 0.8 - - - -
23F ALA* 1.3 76.1 - - - +
25F ARG* 1.3 60.0 + - - +
27F GLY* 3.3 12.7 + - - +
28F GLN 3.8 10.1 + - - +
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Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F GLU* 3.0 42.2 + - - +
21F MET* 3.5 32.6 + - - +
22F LEU* 3.3 28.1 + - - +
24F ALA* 1.3 79.2 - - - +
26F LYS* 1.3 60.4 + - + +
27F GLY 3.2 2.6 + - - -
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Residues in contact with LYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 3.6 28.3 + - - +
23F ALA* 3.2 9.0 + - - +
25F ARG* 1.3 76.7 - - + +
27F GLY* 1.3 61.0 + - - -
28F GLN* 3.2 23.0 + - + +
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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
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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