Contacts of the helix formed by residues 5 - 22 (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 SER 5 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F VAL* 1.3 80.5 - - - +
6F GLY* 1.3 56.0 + - - +
8F ALA* 3.3 6.1 + - - +
9F ALA* 3.0 30.0 + - - +
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Residues in contact with GLY 6 (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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4F VAL* 3.3 8.0 - - - +
5F SER* 1.3 81.1 - - - +
7F ALA* 1.3 59.9 + - - +
9F ALA* 3.4 6.6 + - - +
10F ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 7 (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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4F VAL* 3.4 24.1 + - + +
5F SER 3.3 0.4 - - - -
6F GLY* 1.3 74.5 - - - +
8F ALA* 1.3 65.7 + - - +
10F ALA* 3.2 15.5 + - - +
11F GLU* 3.3 15.3 + - - +
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Residues in contact with ALA 8 (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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4F VAL 3.0 16.8 + - - +
5F SER* 3.7 6.5 - - - +
6F GLY 3.3 0.2 - - - -
7F ALA* 1.3 77.1 - - - +
9F ALA* 1.3 61.2 + - - +
11F GLU* 3.3 18.8 - - - +
12F ALA* 3.3 22.3 + - - +
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Residues in contact with ALA 9 (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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5F SER* 3.0 17.6 + - - +
6F GLY* 3.8 6.7 - - - +
8F ALA* 1.3 74.9 - - - +
10F ALA* 1.3 59.7 + - - +
12F ALA* 3.8 6.0 - - - +
13F ALA* 3.0 29.3 + - - +
16F ARG* 5.1 0.9 + - - -
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Residues in contact with ALA 10 (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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6F GLY 3.1 13.9 + - - +
7F ALA* 3.5 12.3 - - - +
8F ALA 3.2 0.4 - - - -
9F ALA* 1.3 78.1 - - - +
11F GLU* 1.3 58.1 + - - +
13F ALA* 3.3 6.9 + - - +
14F LEU* 2.8 28.7 + - - +
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Residues in contact with GLU 11 (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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363D PRO* 4.9 7.1 - - + +
7F ALA 3.3 10.4 + - - +
8F ALA* 3.3 23.4 - - - +
10F ALA* 1.3 76.1 - - - +
12F ALA* 1.3 63.3 + - + +
14F LEU* 3.5 13.9 - - + +
15F MET* 2.8 35.8 + - + +
52F TRP* 3.2 33.4 + - + +
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Residues in contact with ALA 12 (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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363D PRO* 4.8 11.9 - - + -
364D GLU 5.9 1.8 - - - +
365D ILE* 4.9 2.9 - - + +
8F ALA 3.3 13.6 + - - +
9F ALA* 3.8 7.9 - - - +
10F ALA 3.3 1.0 - - - -
11F GLU* 1.3 83.1 - - + +
13F ALA* 1.3 57.1 + - - +
15F MET* 4.1 4.2 - - - +
16F ARG* 3.0 44.9 + - - +
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Residues in contact with ALA 13 (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 ALA 3.0 18.3 + - - +
10F ALA* 3.7 5.2 - - - +
12F ALA* 1.3 75.5 - - - +
14F LEU* 1.3 58.2 - - - +
16F ARG* 3.3 24.8 - - - +
17F ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 14 (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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10F ALA 2.8 18.4 + - - +
11F GLU* 3.2 14.8 + - + +
13F ALA* 1.3 74.8 - - - +
15F MET* 1.3 73.6 + - + +
17F ALA* 3.0 18.7 + - + +
18F LEU* 3.1 20.2 + - + +
58F ILE* 3.5 40.2 - - + -
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Residues in contact with MET 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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363D PRO* 3.5 21.1 - - + -
365D ILE* 3.7 16.8 - - + -
366D ILE* 3.6 26.0 - - + -
11F GLU* 2.8 24.3 + - + +
12F ALA 4.2 1.1 - - - +
14F LEU* 1.3 78.4 - - + +
16F ARG* 1.3 57.9 + - - +
18F LEU* 3.2 38.3 - - + +
19F TYR* 2.9 44.6 + - + -
48F LEU 3.6 13.9 - - - +
51F ALA 4.8 0.7 - - - +
52F TRP* 3.8 27.1 - - + -
58F ILE* 6.3 0.2 - - - -
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Residues in contact with ARG 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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238D GLU* 4.3 17.5 - - - -
239D ASN* 5.5 3.0 + - - -
242D ARG* 3.9 36.6 - - - +
365D ILE* 4.4 19.9 - - + +
9F ALA 5.1 0.8 + - - -
12F ALA* 3.0 47.6 + - - +
13F ALA* 3.3 28.1 + - - +
15F MET* 1.3 75.8 - - - +
17F ALA* 1.3 59.7 + - - +
19F TYR* 3.3 7.3 + - + +
20F ASP* 2.8 47.6 + - - +
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Residues in contact with ALA 17 (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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13F ALA 2.9 15.3 + - - +
14F LEU* 3.0 15.9 + - + +
16F ARG* 1.3 77.0 - - - +
18F LEU* 1.3 60.8 + - - +
20F ASP* 3.2 15.6 + - - +
21F GLU* 3.3 23.0 + - - +
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Residues in contact with LEU 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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14F LEU* 3.1 23.6 + - + +
15F MET* 3.2 50.7 - - + +
17F ALA* 1.3 75.0 - - - +
19F TYR* 1.3 74.2 + - + +
22F HIS* 3.1 47.3 + - + +
23F ALA* 3.5 2.1 + - - +
48F LEU* 3.7 25.4 - - + +
51F ALA* 4.4 14.4 - - + -
58F ILE* 4.8 10.8 - - + -
69F LEU* 5.8 2.0 - - + -
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Residues in contact with TYR 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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365D ILE* 3.8 32.8 - - + -
366D ILE* 3.4 32.8 - - + +
369D ASN* 4.2 12.1 - - - -
15F MET* 2.9 36.1 + - + +
16F ARG* 3.6 9.4 - - + +
17F ALA 3.3 0.2 - - - -
18F LEU* 1.3 82.9 - - + +
20F ASP* 1.3 63.9 + - - +
23F ALA* 3.2 32.5 - - + +
24F ALA* 4.7 1.4 + - - +
44F VAL* 5.3 2.0 - - + -
45F GLN* 3.3 37.2 + - - -
48F LEU* 3.5 27.3 - - + +
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Residues in contact with ASP 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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284C GLY 4.2 9.9 - - - +
286C PRO* 3.8 17.5 - - - +
16F ARG* 2.8 39.1 + - - +
17F ALA* 3.2 7.6 + - - +
18F LEU 3.1 0.4 - - - -
19F TYR* 1.3 85.6 - - - +
21F GLU* 1.3 64.6 + - + +
22F HIS 3.7 0.4 - - - -
23F ALA 5.0 0.2 - - - -
24F ALA* 5.7 1.9 + - - +
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Residues in contact with GLU 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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286C PRO* 4.6 21.4 - - + +
17F ALA* 3.3 18.1 + - - +
20F ASP* 1.3 83.1 - - + +
22F HIS* 1.3 80.5 + - + +
23F ALA 4.0 0.2 - - - -
24F ALA 5.5 0.4 - - - -
25F VAL* 3.9 6.8 - - - +
66F ARG* 3.3 23.2 + - - -
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Residues in contact with HIS 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 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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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