Contacts of the helix formed by residues 22 - 35 (chain F) in PDB entry 6DVD
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 HIS 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F LEU* 3.1 34.1 + - + +
20F ASP 3.7 0.2 - - - -
21F GLU* 1.3 103.2 + - + +
23F ALA* 1.3 55.9 + - - +
24F ALA 3.5 1.8 - - - -
25F VAL* 3.2 6.3 + - - +
26F LEU* 2.6 40.8 + - + +
48F LEU* 5.5 2.2 - - + -
65F ALA* 5.2 7.1 - - + +
66F ARG* 3.3 48.3 + - + +
69F LEU* 3.8 26.5 - - + -
70F PHE* 5.9 0.2 - - - -
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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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18F LEU 3.5 3.0 + - - -
19F TYR* 3.2 42.7 + - + +
22F HIS* 1.3 77.2 - - - +
24F ALA* 1.3 58.6 + - - +
26F LEU* 3.2 6.3 + - - +
27F TRP* 3.0 29.6 + - - +
44F VAL* 4.3 15.0 - - + +
48F LEU* 4.3 11.0 - - + -
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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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283C PRO 4.7 3.6 - - - +
284C GLY* 3.4 30.1 - - - +
285C GLU* 4.0 18.4 - - + +
19F TYR 4.7 1.6 + - - +
20F ASP 5.7 2.1 + - - +
21F GLU 5.5 0.4 - - - -
22F HIS 4.8 0.6 - - - +
23F ALA* 1.3 79.2 - - - +
25F VAL* 1.3 60.1 + - + +
27F TRP* 3.8 14.7 + - - +
28F ARG* 3.8 17.0 + - - +
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Residues in contact with VAL 25 (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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285C GLU* 4.1 26.7 - - + +
286C PRO* 5.6 3.6 - - + -
21F GLU 3.9 10.5 - - - +
22F HIS 3.2 5.8 + - - +
23F ALA 3.2 0.6 - - - -
24F ALA* 1.3 78.2 - - + +
26F LEU* 1.3 63.6 + - - +
27F TRP 3.2 0.8 + - - -
28F ARG* 3.6 10.4 + - - +
29F TYR* 3.6 11.4 + - - +
66F ARG* 3.4 39.7 - - - +
70F PHE* 4.2 8.7 - - + -
9H G 3.5 41.3 - - + +
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Residues in contact with LEU 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 HIS* 2.6 23.5 + - + +
23F ALA* 3.8 4.3 - - - +
25F VAL* 1.3 70.9 - - - +
27F TRP* 1.3 63.9 + - - +
29F TYR* 3.3 3.8 + - + +
30F ALA* 3.3 21.9 + - + +
43F VAL* 6.0 0.7 - - + -
44F VAL* 4.3 19.7 - - + +
47F THR* 3.9 31.9 - - + +
48F LEU* 4.4 15.0 - - + -
69F LEU* 4.1 27.8 - - + +
70F PHE* 3.8 32.0 - - + -
73F ALA* 4.1 13.9 - - + -
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Residues in contact with TRP 27 (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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23F ALA 3.0 16.2 + - - +
24F ALA* 3.9 9.2 - - - +
25F VAL 3.2 0.2 - - - -
26F LEU* 1.3 78.9 - - - +
28F ARG* 1.3 88.7 + - + +
30F ALA* 3.5 0.6 + - - -
31F LEU* 3.0 56.2 + - + +
37F ALA* 3.5 32.9 + - + -
40F ALA* 3.4 32.0 - - + +
41F GLU* 3.8 26.8 - - + +
44F VAL* 3.9 11.9 - - + +
10H T 4.4 13.0 - + - -
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Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C LYS* 6.2 0.8 - - - +
281C LEU* 4.5 7.1 + - - +
282C ARG* 3.4 55.6 - - - +
283C PRO* 6.1 0.2 - - - +
285C GLU* 5.1 1.4 + - - +
24F ALA 3.8 9.6 + - - +
25F VAL 3.6 5.0 + - - +
26F LEU 3.4 0.2 - - - -
27F TRP* 1.3 103.5 - - + +
29F TYR* 1.3 60.5 + - - +
31F LEU* 3.8 8.9 - - - +
32F ARG* 3.3 25.1 + - - +
9H G 3.6 36.3 - - + +
10H T 3.5 40.7 + - - +
11H A 5.6 3.0 - - - +
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Residues in contact with TYR 29 (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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398C ARG* 3.2 26.6 + - - -
402C GLU* 4.9 5.5 + - - -
25F VAL 3.6 3.8 + - - +
26F LEU* 3.3 9.6 + - + +
27F TRP 3.2 1.0 - - - -
28F ARG* 1.3 76.1 - - - +
30F ALA* 1.3 68.0 + - - +
31F LEU 3.1 1.1 - - - -
32F ARG* 3.2 14.8 + - - +
33F LEU* 3.3 36.0 + - + +
70F PHE* 3.3 70.3 + + + +
73F ALA* 4.9 3.6 - - + -
74F ARG* 4.0 20.7 - - + +
8H A 4.3 28.9 + + + -
9H G 4.4 15.6 + - - +
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.3 13.5 + - + +
27F TRP 4.2 2.2 - - - +
29F TYR* 1.3 83.7 - - + +
31F LEU* 1.3 57.6 + - - +
32F ARG 3.3 0.2 - - - -
33F LEU* 3.3 0.8 + - - +
34F THR* 3.0 34.4 + - - +
40F ALA* 4.2 12.1 - - + +
43F VAL* 4.1 24.2 - - + -
44F VAL* 5.7 0.9 - - + -
73F ALA* 5.0 2.9 - - + -
77F ILE* 3.7 24.7 - - + -
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Residues in contact with LEU 31 (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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27F TRP* 3.0 43.4 + - + +
28F ARG* 3.8 9.6 - - - +
29F TYR 3.1 0.2 - - - -
30F ALA* 1.3 77.8 - - - +
32F ARG* 1.3 57.9 + - - +
34F THR* 4.0 4.7 - - - -
35F GLY* 2.8 30.7 + - - -
36F ASP 4.2 1.6 - - - -
37F ALA* 3.7 34.8 - - + +
40F ALA* 3.9 7.6 - - + +
10H T 3.3 63.9 + - + +
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Residues in contact with ARG 32 (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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394C SER 5.0 5.3 + - - -
395C ARG* 4.9 13.3 + - - +
398C ARG* 3.1 56.4 + - - +
28F ARG 3.3 5.3 + - - +
29F TYR* 3.2 9.0 + - - +
31F LEU* 1.3 79.9 - - - +
33F LEU* 1.3 60.2 + - - +
34F THR 4.7 0.2 - - - -
35F GLY* 4.4 2.6 + - - -
9H G 3.1 48.0 + - - +
10H T 3.3 41.2 + - - +
11H A 3.5 20.8 + - - +
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Residues in contact with LEU 33 (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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398C ARG* 3.4 32.1 - - - +
29F TYR* 3.5 42.0 - - + +
30F ALA 3.3 2.5 + - - +
32F ARG* 1.3 78.1 - - - +
34F THR* 1.3 61.2 + - - +
74F ARG* 4.4 17.3 - - + +
77F ILE* 3.7 40.0 - - + +
81F ARG* 4.5 15.6 + - - -
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Residues in contact with THR 34 (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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30F ALA* 3.0 18.5 + - + +
31F LEU* 4.0 1.6 - - - -
32F ARG 4.7 0.2 - - - -
33F LEU* 1.3 83.0 - - - +
35F GLY* 1.3 61.9 + - - +
36F ASP* 3.2 22.7 + - - +
39F GLN* 3.4 43.1 + - + +
40F ALA 4.5 0.9 + - - -
43F VAL* 5.2 1.1 - - + -
77F ILE* 3.7 26.0 - - + -
81F ARG* 5.2 5.4 + - - +
85F ARG* 5.0 10.2 + - - +
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Residues in contact with GLY 35 (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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392D THR* 4.4 7.6 + - - -
393D GLY 5.4 2.3 - - - +
396D ASN* 5.2 4.0 - - - +
31F LEU* 2.8 27.9 + - - -
32F ARG 4.4 2.1 - - - -
33F LEU 3.9 0.4 - - - -
34F THR* 1.3 72.5 + - - +
36F ASP* 1.3 57.3 + - - +
37F ALA 4.0 1.6 + - - -
10H T 4.6 13.2 - - - +
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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