Contacts of the helix formed by residues 7 - 25 (chain F) in PDB entry 2FYU
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 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F ALA 4.2 7.8 + - - -
6F VAL* 1.3 72.7 - - - +
8F ALA* 1.3 68.7 + - - +
9F SER 3.7 1.3 - - - +
10F SER* 3.6 6.1 + - - +
11F ARG* 3.4 55.4 + - - +
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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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7F SER* 1.3 81.2 + - - +
9F SER* 1.3 64.4 + - - +
11F ARG* 3.8 13.3 + - - +
12F TRP* 3.6 18.7 + - - +
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Residues in contact with SER 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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6F VAL* 6.5 0.9 - - - -
8F ALA* 1.3 75.0 - - - +
10F SER* 1.3 60.0 + - - +
12F TRP* 3.5 6.7 + - - +
13F LEU* 3.1 29.4 + - - +
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Residues in contact with SER 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 VAL* 3.7 37.4 - - - +
7F SER 3.6 10.4 + - - +
8F ALA 3.4 0.2 - - - -
9F SER* 1.3 77.6 - - - +
11F ARG* 1.3 52.6 + - - +
13F LEU* 3.4 14.5 + - - +
14F GLU* 2.8 39.9 + - - +
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Residues in contact with ARG 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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6F VAL 5.2 0.2 + - - -
7F SER* 3.4 46.1 + - - +
8F ALA* 4.1 11.2 - - - +
9F SER 3.5 0.4 - - - -
10F SER* 1.3 77.4 - - - +
12F TRP* 1.3 52.2 + - - +
14F GLU* 3.7 8.6 - - + +
15F GLY* 2.8 27.8 + - - -
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Residues in contact with TRP 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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8F ALA 3.6 10.5 + - - +
9F SER* 3.5 10.9 + - - +
10F SER 3.3 0.4 - - - -
11F ARG* 1.3 76.0 - - - +
13F LEU* 1.3 61.5 + - - +
15F GLY* 3.1 5.9 + - - +
16F ILE* 3.0 60.5 + - + +
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Residues in contact with LEU 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 SER 3.1 14.1 + - - +
10F SER* 3.5 15.5 - - - +
12F TRP* 1.3 75.3 - - - +
14F GLU* 1.3 61.9 + - - +
16F ILE* 3.6 7.3 + - - +
17F ARG* 3.2 65.5 + - - +
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Residues in contact with GLU 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LYS* 3.0 15.6 + - - -
10F SER* 2.8 24.1 + - - +
11F ARG* 3.7 10.8 - - + +
13F LEU* 1.3 72.6 - - - +
15F GLY* 1.3 52.4 + - - +
17F ARG* 3.4 13.0 + - - +
18F LYS* 2.7 37.3 + - + +
83F TYR* 2.8 34.8 + - + +
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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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11F ARG 2.8 19.4 + - - -
12F TRP* 3.1 10.8 + - - -
14F GLU* 1.3 71.1 - - - +
16F ILE* 1.3 55.5 + - - +
18F LYS* 3.5 6.5 + - - +
19F TRP* 2.8 34.8 + - - +
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Residues in contact with ILE 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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376C LEU* 3.7 22.4 - - + +
12F TRP* 3.0 61.8 + - + +
13F LEU* 4.0 7.0 - - - +
15F GLY* 1.3 72.6 - - - +
17F ARG* 1.3 60.0 + - - +
19F TRP* 3.8 17.4 - - + +
20F TYR* 3.0 29.5 + - - +
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Residues in contact with ARG 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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375C LYS* 4.2 10.3 + - - +
376C LEU* 3.3 34.2 + - + +
377C LEU* 5.7 1.0 - - - +
378C LYS* 3.6 45.9 - - - +
13F LEU* 3.2 51.9 + - + +
14F GLU* 3.5 11.3 + - - +
16F ILE* 1.3 74.5 - - - +
18F LYS* 1.3 55.0 + - - +
20F TYR* 3.5 4.7 + - - +
21F TYR* 3.0 28.2 + - - +
83F TYR* 3.5 22.4 - - + +
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Residues in contact with LYS 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 GLU 2.7 21.7 + - - +
15F GLY* 3.8 5.8 - - - +
17F ARG* 1.3 69.8 - - - +
19F TRP* 1.4 63.2 - - - +
21F TYR* 3.5 6.6 + - - +
22F ASN* 3.1 43.1 + - - +
83F TYR* 3.6 29.3 - - + -
84F GLU* 3.2 32.8 + - - +
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Residues in contact with TRP 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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319C PRO* 5.4 6.1 - - + -
320C LEU* 5.3 9.6 - - + -
376C LEU* 5.7 2.0 - - + -
15F GLY 2.8 22.3 + - - +
16F ILE* 3.8 19.7 - - + +
17F ARG 3.5 0.2 - - - -
18F LYS* 1.4 71.2 - - - +
20F TYR* 1.3 93.1 + + + +
22F ASN* 3.4 7.0 + - + +
23F ALA* 3.1 39.4 + - + +
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Residues in contact with TYR 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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312C GLN* 4.8 2.3 + - - -
317C PHE 3.5 14.9 + - - -
318C ARG* 3.8 4.0 - - - +
319C PRO* 3.6 29.2 - - + -
320C LEU* 4.2 10.1 - - + -
373C GLU* 3.2 49.1 + - + +
376C LEU* 3.7 35.4 - - + -
377C LEU* 3.6 33.2 - - + -
16F ILE 3.0 19.6 + - - +
17F ARG 3.8 3.4 - - - +
19F TRP* 1.3 88.2 - + + +
21F TYR* 1.3 59.2 + - - +
23F ALA* 3.8 1.7 - - - -
24F ALA* 2.8 33.4 + - + +
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Residues in contact with TYR 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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377C LEU* 4.2 14.8 - - + -
17F ARG 3.0 17.7 + - - +
18F LYS 3.5 6.3 - - - +
19F TRP 3.3 0.2 - - - -
20F TYR* 1.3 77.6 - - - +
22F ASN* 1.3 71.4 + - - +
24F ALA* 3.4 13.0 + - - +
25F GLY 3.4 9.4 + - - -
26F PHE* 3.5 31.8 - + - -
27F ASN* 3.7 13.1 - - + +
33F ARG* 4.9 2.2 - - + -
81F THR* 2.9 41.2 + - - -
83F TYR* 3.7 43.3 - + + -
86F ASP* 2.7 40.5 + - + +
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Residues in contact with ASN 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 LYS* 3.1 33.5 + - - +
19F TRP* 3.4 8.8 + - + +
20F TYR 3.3 0.2 - - - -
21F TYR* 1.3 83.5 - - - +
23F ALA* 1.3 59.4 + - - +
25F GLY* 3.3 11.3 + - - -
27F ASN* 3.6 24.4 + - - +
28F LYS* 3.4 19.9 + - - -
80F TRP* 5.5 4.8 - - - -
81F THR 5.4 0.4 + - - -
83F TYR* 5.8 2.0 - - - +
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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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319C PRO* 3.8 19.7 - - + +
19F TRP* 3.1 37.0 + - + +
20F TYR* 3.9 4.5 - - - +
22F ASN* 1.3 73.3 - - - +
24F ALA* 1.4 65.5 + - - +
25F GLY* 3.5 1.6 + - - -
28F LYS* 5.1 2.5 + - - +
47G ARG* 2.8 33.7 + - - +
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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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316C MET 3.8 5.2 - - - +
317C PHE* 3.2 46.5 - - - +
319C PRO* 3.9 5.3 - - - +
377C LEU* 5.1 0.2 - - + -
20F TYR* 2.8 32.1 + - + +
21F TYR* 3.4 8.3 + - - +
23F ALA* 1.4 72.9 - - - +
25F GLY* 1.3 61.6 + - - +
26F PHE* 3.4 23.1 - - + -
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Residues in contact with GLY 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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317C PHE* 4.1 4.5 - - - -
21F TYR 3.4 4.2 + - - -
22F ASN 3.3 13.1 + - - -
23F ALA 4.3 1.1 - - - -
24F ALA* 1.3 76.8 - - - +
26F PHE* 1.3 58.6 + - - +
27F ASN* 3.2 12.8 - - - -
28F LYS* 3.1 37.0 + - - +
29F LEU* 4.0 6.2 + - - +
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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