Contacts of the helix formed by residues 3 - 20 (chain B) in PDB entry 3FYA
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 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.3 2.4 - - - +
51A LYS* 4.3 16.4 - - - +
54A GLU* 2.6 26.6 + - - -
4B PHE* 1.3 63.4 + - - +
5B LEU* 3.0 1.2 + - - +
6B LEU* 2.9 43.2 + - - +
7B SER* 3.1 18.4 + - - -
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Residues in contact with PHE 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.9 11.4 + - - +
64A ASP* 3.9 23.3 - - - -
3B SER* 1.3 70.5 - - - +
5B LEU* 1.3 66.2 + - + +
7B SER* 3.1 28.4 + - - -
8B LYS* 3.2 43.0 + - + +
75B ILE* 4.9 19.7 - - + -
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.2 26.9 - - + +
53A LEU* 4.4 6.5 - - + -
54A GLU* 3.6 24.0 + - + +
57A MET* 3.5 26.9 - - + -
64A ASP* 3.4 24.7 - - + +
68A PHE* 3.8 29.6 - - + -
3B SER* 3.0 1.6 + - - +
4B PHE* 1.3 77.6 - - + +
6B LEU* 1.3 67.9 + - - +
8B LYS* 2.7 20.1 + - + +
9B VAL* 3.0 23.6 + - + -
71B LEU* 5.1 4.9 - - + -
75B ILE* 5.5 2.0 - - + -
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.6 27.5 - - + +
51A LYS* 4.1 21.1 - - + -
3B SER* 2.9 33.5 + - - +
5B LEU* 1.3 70.8 - - - +
7B SER* 1.3 62.6 + - - +
9B VAL* 4.6 3.6 - - - -
10B SER* 2.8 31.2 + - - -
41B ILE 5.6 0.2 - - - +
44B ASN 4.9 1.8 - - - +
45B SER* 3.0 44.0 - - - +
46B ARG 3.9 11.2 - - - +
47B ASN* 4.5 5.2 - - - +
48B LEU* 3.9 17.5 - - + -
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER 3.1 8.2 + - - -
4B PHE* 3.1 20.0 + - - -
5B LEU 2.9 4.2 + - - -
6B LEU* 1.3 76.0 - - - +
8B LYS* 1.3 78.4 + - - -
10B SER* 3.8 2.8 + - - -
11B PHE* 3.1 27.9 + - - +
45B SER* 4.1 9.8 + - - -
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.2 39.9 + - + +
5B LEU* 2.7 15.9 + - + +
7B SER* 1.3 91.6 + - - +
9B VAL* 1.3 60.8 + - - +
11B PHE* 3.9 7.1 - - + +
12B VAL* 3.0 32.3 + - - +
71B LEU* 4.2 6.1 - - + +
74B GLU* 3.2 51.1 - - + +
75B ILE* 3.8 15.7 - - + +
77B LYS 5.6 1.6 - - - -
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.0 8.5 - - + -
68A PHE* 5.2 4.9 - - + -
5B LEU* 3.0 30.9 + - + +
6B LEU* 3.9 7.9 - - - +
8B LYS* 1.3 71.2 - - - +
10B SER* 1.3 69.9 + - - +
12B VAL* 2.9 15.4 + - - +
13B ILE* 3.0 27.3 + - + +
48B LEU* 4.5 17.7 - - + -
53B LEU* 4.6 15.5 - - + -
67B PHE* 4.4 13.0 - - + -
68B PHE* 6.2 0.7 - - + -
71B LEU* 3.4 25.8 - - + +
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Residues in contact with SER 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 2.8 25.1 + - - +
7B SER 3.8 3.9 + - - -
9B VAL* 1.3 74.6 - - - +
11B PHE* 1.3 63.7 + - - +
13B ILE* 3.1 15.7 - - - +
14B LYS* 3.1 21.8 + - - +
41B ILE* 3.3 31.1 + - - -
42B GLU* 3.4 19.6 + - - +
45B SER* 4.0 9.1 + - - -
48B LEU* 6.0 1.5 - - - +
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER 3.1 20.5 + - - +
8B LYS* 3.9 11.0 - - + +
9B VAL 3.1 0.2 - - - -
10B SER* 1.3 79.1 + - - +
12B VAL* 1.3 57.5 + - - +
14B LYS* 3.4 14.2 + - + +
15B LYS* 3.0 43.6 + - + +
74B GLU* 3.3 43.1 - - + -
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS 3.0 18.8 + - - +
9B VAL 2.9 4.5 + - - +
11B PHE* 1.3 75.5 - - - +
13B ILE* 1.3 57.3 + - - +
15B LYS* 3.5 10.0 - - + +
16B ILE* 2.8 50.9 + - + +
67B PHE* 4.1 15.0 - - + +
70B MET* 3.5 48.2 - - + +
71B LEU* 3.8 13.7 - - + -
74B GLU* 3.9 15.0 - - + -
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.0 21.6 + - + +
10B SER* 3.1 12.1 - - - +
12B VAL* 1.3 74.1 - - - +
14B LYS* 1.3 62.7 + - - +
16B ILE 3.9 0.2 - - - -
17B ARG* 2.9 30.8 + - - +
27B LEU* 4.6 13.2 - - + -
38B ILE* 5.8 0.9 - - + -
41B ILE* 4.3 14.8 - - + -
42B GLU* 3.3 26.7 - - + +
48B LEU* 4.5 3.8 - - + -
53B LEU* 4.3 15.5 - - + -
56B ILE* 4.0 31.9 - - + -
60B LEU* 3.9 9.5 - - + +
67B PHE* 4.2 18.6 - - + -
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Residues in contact with LYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B SER 3.1 8.4 + - - +
11B PHE* 3.7 18.4 - - + +
13B ILE* 1.3 77.7 - - - +
15B LYS* 1.3 54.3 + - - +
17B ARG* 3.2 22.3 + - - +
18B LEU* 2.7 57.3 + - + +
24B GLN* 5.9 0.9 - - - +
42B GLU* 3.4 38.6 - - + +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.0 33.8 + - + +
12B VAL* 3.5 17.5 - - + +
14B LYS* 1.3 76.4 - - - +
16B ILE* 1.3 55.5 + - + +
18B LEU* 3.3 9.3 + - - +
19B GLU* 2.7 54.2 + - + +
70B MET* 5.0 11.1 + - + +
73B LYS* 4.8 12.5 - - - +
74B GLU* 2.8 36.6 + - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 2.8 36.5 + - + +
15B LYS* 1.3 72.7 - - + +
17B ARG* 1.3 56.8 + - - +
19B GLU* 3.0 17.1 + - + +
20B LYS* 2.6 47.4 + - + +
60B LEU* 4.0 12.8 - - + -
62B VAL* 3.8 29.6 - - + -
66B VAL* 6.2 0.4 - - + -
67B PHE* 3.8 23.8 - - + -
70B MET* 3.7 25.8 - - + -
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Residues in contact with ARG 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE 2.9 22.8 + - - +
14B LYS* 3.3 25.2 - - - +
16B ILE* 1.3 73.2 - - - +
18B LEU* 1.3 75.5 + - - +
20B LYS* 3.4 1.1 + - - -
22B MET* 2.9 66.1 + - + +
23B THR* 3.6 24.4 - - - +
24B GLN* 3.8 19.6 - - - +
27B LEU* 4.0 15.9 - - + -
38B ILE* 4.9 0.2 - - - -
42B GLU* 2.9 42.1 + - - -
60B LEU* 3.4 14.8 - - + +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 2.7 55.4 + - + +
15B LYS* 3.4 7.9 - - - +
17B ARG* 1.3 89.8 - - - +
19B GLU* 1.3 65.6 + - - +
20B LYS 3.0 1.6 - - - -
21B GLY* 3.0 15.2 + - - -
22B MET 4.4 3.8 - - - +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS* 2.7 43.2 + - + +
16B ILE* 3.0 23.0 + - + +
18B LEU* 1.3 71.5 - - - +
20B LYS* 1.3 58.9 + - + +
21B GLY 3.2 5.2 + - - -
70B MET* 4.3 17.8 - - - +
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Residues in contact with LYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 2.6 30.5 + - + +
17B ARG* 3.7 5.8 - - - +
18B LEU 3.0 0.8 - - - -
19B GLU* 1.3 73.1 - - + +
21B GLY* 1.3 63.8 + - - +
22B MET* 2.9 35.9 + - + +
60B LEU* 3.1 29.6 - - - +
61B GLU* 3.7 23.3 - - - +
62B VAL* 5.6 0.4 - - - -
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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
------------------------------------------------------------
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