Contacts of the helix formed by residues 11 - 28 (chain F) in PDB entry 4GDK
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 PRO 11 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F HIS* 4.4 11.2 - - + +
10F MET* 1.3 92.4 - - + +
12F ARG* 1.3 60.9 + - - +
13F TRP* 3.3 41.7 - - + +
14F LYS* 3.3 16.6 + - + +
15F ARG* 3.0 24.3 + - - +
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Residues in contact with ARG 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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246E MET* 4.2 7.6 - - + +
248E GLU* 4.6 11.0 - - - +
9F HIS* 5.0 17.7 + - + +
10F MET 4.6 0.7 - - - +
11F PRO* 1.3 73.7 - - + +
13F TRP* 1.3 58.8 + - - +
15F ARG* 3.5 12.5 + - - +
16F HIS* 3.0 28.8 + - - +
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Residues in contact with TRP 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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246E MET* 3.7 21.4 - - - +
248E GLU* 4.1 24.2 + - + +
249E THR* 3.6 29.4 - - + +
250E PRO* 3.4 35.1 - - + +
253E TRP* 3.5 43.3 - + + -
11F PRO* 3.3 32.1 - - + +
12F ARG* 1.3 80.2 - - - +
14F LYS* 1.3 99.3 + - + +
16F HIS* 3.6 3.3 + - - +
17F ILE* 3.2 32.9 + - + +
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Residues in contact with LYS 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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3E ASP 5.7 4.0 - - - +
4E ASP* 3.0 34.2 + - - +
7E VAL* 5.6 2.2 - - + +
253E TRP* 3.4 31.9 - - + +
10F MET* 3.8 30.5 - - + -
11F PRO* 3.3 19.0 + - + +
12F ARG 3.2 0.2 - - - -
13F TRP* 1.3 104.3 - - + +
15F ARG* 1.3 63.7 + - - +
17F ILE* 3.4 6.5 + - - +
18F SER* 3.1 27.0 + - - +
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Residues in contact with ARG 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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9F HIS* 3.9 17.0 + - - +
10F MET* 3.0 54.6 + - - +
11F PRO 3.0 13.4 + - - +
12F ARG* 3.7 11.7 - - - +
14F LYS* 1.3 76.2 - - - +
16F HIS* 1.3 62.1 - - - +
18F SER* 3.4 4.2 + - - -
19F GLU* 3.1 50.8 + - + +
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Residues in contact with HIS 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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244E GLU 3.0 26.1 + - - -
245E PRO* 4.1 4.7 - - + -
246E MET* 3.7 33.6 - - + +
12F ARG 3.0 18.6 + - - +
13F TRP* 3.6 8.3 - - - +
14F LYS 3.2 0.2 - - - -
15F ARG* 1.3 78.0 - - - +
17F ILE* 1.3 59.3 + - - +
19F GLU* 3.4 9.1 + - - +
20F GLN* 3.0 62.5 + - + +
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Residues in contact with ILE 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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7E VAL* 4.4 3.8 - - + -
243E ILE* 3.8 20.0 - - + -
245E PRO* 4.1 28.0 - - + -
249E THR* 4.0 19.1 - - + +
253E TRP* 3.5 32.5 - - + -
254E LEU* 4.2 7.0 - - + -
258E LEU* 4.2 12.8 - - + -
13F TRP* 3.2 17.7 + - + +
14F LYS* 3.8 4.9 - - - +
15F ARG 3.3 0.2 - - - -
16F HIS* 1.3 79.8 - - + +
18F SER* 1.3 63.6 + - - +
20F GLN* 3.3 2.1 + - - +
21F LEU* 3.0 37.7 + - + +
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Residues in contact with SER 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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3E ASP 5.0 2.3 + - - -
7E VAL* 3.7 21.0 - - - +
10E ASP* 4.9 1.6 - - - +
10F MET* 4.7 10.0 - - - +
14F LYS* 3.1 18.6 + - - +
15F ARG* 3.7 6.3 - - - -
17F ILE* 1.3 77.8 - - - +
19F GLU* 1.3 62.9 + - - +
21F LEU* 3.5 8.2 + - - +
22F ARG* 3.2 48.8 + - - +
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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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274B THR 4.1 10.6 - - - +
275B ASP* 3.7 29.2 - - - +
15F ARG* 3.1 43.3 + - + +
16F HIS* 3.8 7.2 + - - +
18F SER* 1.3 73.9 - - - +
20F GLN* 1.3 63.0 + - + +
22F ARG* 3.3 18.7 + - - +
23F ARG* 2.8 30.5 + - - +
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Residues in contact with GLN 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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275B ASP 5.8 1.6 + - - -
243E ILE* 3.5 26.4 - - + +
244E GLU* 4.3 15.7 + - - +
16F HIS* 3.0 53.9 + - + +
17F ILE 3.3 4.5 + - - +
19F GLU* 1.3 76.8 - - - +
21F LEU* 1.3 61.6 + - - +
23F ARG* 3.4 26.9 + - - +
24F ARG* 2.9 28.2 + - - +
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Residues in contact with LEU 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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7E VAL* 3.8 30.1 - - + -
10E ASP* 4.1 21.3 - - + +
11E VAL* 4.0 20.9 - - + -
241E HIS* 4.3 4.0 - - + +
243E ILE* 3.7 24.9 - - + -
258E LEU* 4.6 0.7 - - + -
17F ILE* 3.0 28.4 + - + +
18F SER* 3.8 6.5 - - - +
20F GLN* 1.3 78.2 - - - +
22F ARG* 1.3 57.2 + - - +
24F ARG* 3.3 34.1 + - - +
25F ASP* 3.0 34.2 + - - +
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Residues in contact with ARG 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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275B ASP* 3.9 23.6 - - + +
6E ASP* 6.2 2.4 - - - +
10E ASP* 3.9 19.2 + - - +
18F SER* 3.2 33.8 + - - +
19F GLU* 3.8 26.1 - - - +
21F LEU* 1.3 73.6 - - - +
23F ARG* 1.3 65.2 + - - +
25F ASP* 3.5 9.6 + - - +
26F ARG* 3.2 22.9 + - - +
30F GLN* 4.9 2.3 + - - -
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Residues in contact with ARG 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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275B ASP* 3.9 15.1 + - - +
23C ARG* 4.0 23.2 - - - +
19F GLU 2.8 18.1 + - - +
20F GLN* 3.5 28.5 + - - +
22F ARG* 1.3 77.0 - - - +
24F ARG* 1.3 61.8 + - - +
26F ARG* 3.3 28.9 + - - +
27F LEU* 3.1 57.8 + - + +
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Residues in contact with ARG 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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10E ASP* 2.8 31.1 + - - +
11E VAL* 4.3 2.8 - - - +
14E GLY* 3.6 9.8 - - - -
15E ARG 5.9 0.2 + - - -
41E ARG* 3.5 33.0 - - - +
241E HIS* 2.6 44.8 + - - +
242E GLY* 4.3 9.2 - - - +
243E ILE* 4.4 5.6 - - + -
20F GLN 2.9 18.1 + - - +
21F LEU* 3.4 22.5 + - - +
23F ARG* 1.3 75.2 - - - +
25F ASP* 1.3 82.6 + - - +
27F LEU* 3.2 6.4 + - - -
28F GLN* 2.8 60.2 + - - +
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Residues in contact with ASP 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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10E ASP* 4.1 24.2 - - - +
13E PHE 5.9 0.9 - - - -
14E GLY* 4.6 6.3 - - - -
15E ARG 5.3 0.5 + - - -
21F LEU 3.0 20.0 + - - +
22F ARG* 3.8 8.5 - - - +
23F ARG 3.4 0.2 - - - -
24F ARG* 1.3 104.0 + - - +
26F ARG* 1.3 57.5 + - - +
28F GLN* 5.1 0.4 - - - -
29F ARG* 3.1 22.6 + - + +
30F GLN* 2.8 44.5 + - + +
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Residues in contact with ARG 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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92B SER 5.7 0.6 + - - -
93B SER* 3.4 29.5 + - - +
94B SER* 4.6 2.8 + - - +
95B ALA* 3.9 30.1 - - + +
96B LEU 5.0 0.5 + - - -
273B PRO* 4.8 15.1 - - - +
275B ASP* 2.4 43.0 + - - +
22F ARG 3.2 13.5 + - - +
23F ARG* 3.5 29.1 - - - +
24F ARG 3.1 0.6 - - - -
25F ASP* 1.3 79.9 - - - +
27F LEU* 1.3 81.4 + - + +
28F GLN 3.6 0.2 + - - -
30F GLN* 3.9 16.4 - - - +
31F ALA* 3.7 17.7 + - - +
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Residues in contact with LEU 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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96B LEU* 6.6 0.4 - - + -
23C ARG* 6.0 1.3 - - - +
27C LEU* 6.0 9.9 - - + -
96E LEU* 3.8 11.3 - - - +
23F ARG* 3.1 59.2 + - + +
24F ARG* 3.9 4.9 - - - +
26F ARG* 1.3 98.1 - - + +
28F GLN* 1.3 65.0 + - + +
31F ALA* 3.6 14.9 - - - +
32F PHE* 4.7 0.7 - - - -
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Residues in contact with GLN 28 (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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15E ARG 4.1 12.8 - - - +
16E ILE* 4.7 1.7 - - - +
17E PRO* 3.4 23.0 - - + +
41E ARG* 3.0 32.3 + - - +
87E PHE* 3.8 21.7 - - - -
92E SER* 5.9 1.4 - - - -
96E LEU* 3.8 18.9 - - + +
242E GLY* 5.5 2.8 + - - -
24F ARG* 2.8 34.4 + - + +
25F ASP* 5.1 0.4 - - - -
26F ARG 3.3 0.2 - - - -
27F LEU* 1.3 85.5 - - + +
29F ARG* 1.3 66.2 + - - +
31F ALA 3.7 2.0 + - - -
32F PHE* 3.6 11.6 - - - -
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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