Contacts of the helix formed by residues 11 - 29 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C MET* 1.3 94.5 - - + +
12C ARG* 1.3 66.6 + - - +
13C TRP* 3.5 40.6 - - + +
14C LYS* 3.2 18.0 + - + +
15C ARG* 3.1 19.2 + - - +
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Residues in contact with ARG 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET* 3.9 21.9 - - + +
248B GLU* 2.7 41.4 + - - +
10C MET 3.6 1.5 + - - -
11C PRO* 1.3 72.4 - - - +
13C TRP* 1.3 59.5 + - + +
15C ARG* 3.6 7.6 + - - +
16C HIS* 3.1 24.9 + - - +
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Residues in contact with TRP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B MET* 3.8 21.9 + - + -
248B GLU* 3.8 26.0 + - + -
249B THR* 3.6 31.9 + - + +
250B PRO* 3.4 33.0 - - + +
253B TRP* 3.6 41.7 - + - -
11C PRO* 3.5 27.7 - - + +
12C ARG* 1.3 78.9 - - + +
14C LYS* 1.3 107.2 + - + +
16C HIS* 3.5 3.6 - - - +
17C ILE* 3.3 27.6 + - + +
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Residues in contact with LYS 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ASP 5.6 2.5 - - - +
4B ASP* 2.7 36.6 + - - +
7B VAL* 5.1 4.8 - - + +
253B TRP* 3.8 30.0 - - + +
10C MET* 4.0 26.2 - - + -
11C PRO* 3.2 23.6 + - + +
13C TRP* 1.3 101.9 - - + +
15C ARG* 1.3 64.6 + - - +
16C HIS 3.2 0.2 - - - -
17C ILE* 3.3 5.9 + - - +
18C SER* 3.2 26.5 + - - +
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Residues in contact with ARG 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MET* 3.8 49.5 + - - +
11C PRO 3.1 14.4 + - - +
12C ARG* 3.8 8.0 - - - +
14C LYS* 1.3 75.5 - - - +
16C HIS* 1.3 64.0 - - - +
18C SER* 3.5 3.0 + - - -
19C GLU* 3.0 51.4 + - + +
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Residues in contact with HIS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 6.3 0.2 - - + -
244B GLU 3.1 27.5 + - - -
245B PRO* 4.3 3.8 - - + -
246B MET* 3.9 43.2 - - + +
12C ARG 3.1 14.8 + - - +
13C TRP* 3.5 10.5 - - - +
14C LYS 3.2 0.2 - - - -
15C ARG* 1.3 77.7 - - - +
17C ILE* 1.3 59.8 + - + +
19C GLU* 3.4 10.4 + - - +
20C GLN* 2.9 61.3 + - + +
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Residues in contact with ILE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.4 10.5 - - + -
243B ILE* 3.8 23.7 - - + +
245B PRO* 4.5 23.1 - - + -
246B MET 5.5 0.2 - - - +
249B THR* 4.2 15.9 - - + +
253B TRP* 3.5 28.3 - - + -
254B LEU* 4.5 6.3 - - + -
258B LEU* 4.3 14.1 - - + -
13C TRP* 3.3 16.2 + - + +
14C LYS* 3.8 7.4 - - - +
15C ARG 3.3 0.4 - - - -
16C HIS* 1.3 76.0 - - + +
18C SER* 1.3 60.2 + - - +
20C GLN* 3.3 1.9 + - - +
21C LEU* 2.9 45.1 + - + +
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ASP 5.3 1.4 + - - -
6B ASP* 5.8 2.8 - - - +
7B VAL* 3.7 20.5 - - - +
10B ASP* 4.8 5.0 + - - +
10C MET* 4.9 10.2 - - - +
14C LYS* 3.2 16.5 + - - +
15C ARG* 3.8 6.5 - - - -
17C ILE* 1.3 80.3 - - - +
19C GLU* 1.3 62.4 + - - +
21C LEU* 3.5 4.9 + - - +
22C ARG* 3.1 47.5 + - - +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 3.0 47.2 + - + +
16C HIS* 3.8 12.3 + - - +
18C SER* 1.3 75.5 - - - +
20C GLN* 1.3 64.3 + - - +
22C ARG* 3.4 26.4 + - - +
23C ARG* 2.9 28.8 + - - +
274E THR* 5.1 15.2 - - + +
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ILE* 3.7 28.0 - - + +
244B GLU* 4.9 8.5 + - - +
16C HIS* 2.9 50.8 + - + +
17C ILE 3.3 3.3 + - - +
19C GLU* 1.3 81.0 - - - +
21C LEU* 1.3 58.7 + - - +
23C ARG* 3.3 27.7 + - - +
24C ARG* 2.8 30.0 + - - +
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.2 11.0 - - + +
10B ASP* 3.8 31.9 - - + +
11B VAL* 4.1 22.4 - - + -
241B HIS* 4.3 3.6 - - + +
243B ILE* 3.7 25.1 - - + -
258B LEU* 4.9 1.1 - - + -
17C ILE* 2.9 37.6 + - + +
18C SER* 3.9 4.7 - - - +
20C GLN* 1.3 75.4 - - - +
22C ARG* 1.3 62.4 + - - +
24C ARG* 3.3 33.5 + - - +
25C ASP* 3.1 32.1 + - - +
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Residues in contact with ARG 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 4.5 14.1 - - - +
18C SER* 3.1 43.9 + - - +
19C GLU* 3.4 30.4 + - - +
20C GLN 3.3 0.2 - - - -
21C LEU* 1.3 73.5 - - - +
23C ARG* 1.3 65.2 + - - +
25C ASP* 3.5 7.1 + - - +
26C ARG* 3.1 33.4 + - - +
274E THR* 6.0 2.6 - - - +
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Residues in contact with ARG 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU 2.9 18.1 + - - +
20C GLN* 3.3 28.5 + - - +
22C ARG* 1.3 76.2 - - - +
24C ARG* 1.3 63.4 + - - +
26C ARG* 3.4 28.2 + - - +
27C LEU* 3.1 61.4 + - + +
23F ARG* 4.0 23.4 - - - +
27F LEU* 6.0 1.2 - - - +
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 2.8 29.5 + - - +
11B VAL* 4.8 3.0 - - - +
14B GLY* 3.6 11.4 - - - -
15B ARG 5.7 0.2 - - - +
41B ARG* 3.5 32.2 - - - +
241B HIS* 2.9 36.8 + - - +
242B GLY* 4.4 7.2 - - - +
243B ILE* 4.3 9.0 - - + -
20C GLN 2.8 18.2 + - - +
21C LEU* 3.5 20.8 + - - +
23C ARG* 1.3 76.5 - - - +
25C ASP* 1.3 83.9 + - - +
27C LEU* 3.4 5.4 + - - -
28C GLN* 2.8 57.9 + - - +
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Residues in contact with ASP 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 3.9 19.2 - - - +
13B PHE 5.8 1.8 - - - -
14B GLY* 4.8 4.6 - - - -
15B ARG 5.2 1.7 + - - -
21C LEU 3.1 15.7 + - - +
22C ARG* 3.9 7.1 - - - +
23C ARG 3.4 0.2 - - - -
24C ARG* 1.3 106.4 + - - +
26C ARG* 1.3 60.6 + - - +
28C GLN* 5.1 0.7 - - - -
29C ARG* 2.7 40.2 + - + +
30C GLN* 2.9 12.0 + - - -
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 3.1 34.5 + - - +
23C ARG* 3.7 32.3 + - - +
25C ASP* 1.3 75.5 - - - +
27C LEU* 1.3 70.0 + - + +
30C GLN* 3.6 27.0 - - - +
31C ALA* 3.4 22.0 + - - +
93E SER 5.0 12.7 + - - -
94E SER* 6.0 0.2 - - - +
95E ALA* 4.2 21.9 - - + +
274E THR 3.4 25.8 + - - -
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Residues in contact with LEU 27 (chain C).
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* 3.8 13.7 - - + +
23C ARG* 3.1 59.9 + - + +
24C ARG* 3.9 5.4 - - - +
26C ARG* 1.3 87.0 - - + +
28C GLN* 1.3 64.3 + - + +
31C ALA* 3.4 19.7 - - - +
32C PHE* 4.2 1.4 - - - -
27F LEU* 6.0 9.2 - - + -
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Residues in contact with GLN 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG 4.1 13.5 - - - +
16B ILE* 4.7 2.0 - - - +
17B PRO* 3.2 32.7 - - + +
38B LEU* 4.6 0.3 - - - +
41B ARG* 3.1 34.0 + - - +
87B PHE* 4.0 19.2 - - - -
92B SER 5.9 0.6 + - - -
96B LEU* 3.9 21.4 - - + +
242B GLY* 5.3 3.8 + - - -
24C ARG* 2.8 33.5 + - - +
25C ASP* 5.1 0.7 - - - -
27C LEU* 1.3 84.5 - - + +
29C ARG* 1.3 60.2 + - - +
32C PHE* 3.6 9.2 - - - +
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.2 35.8 + - - +
15B ARG* 3.6 47.2 - - + +
38B LEU* 4.3 11.1 - - + +
25C ASP* 2.7 29.6 + - + +
28C GLN* 1.3 72.8 - - - +
30C GLN* 1.3 59.4 + - - +
31C ALA 3.2 1.8 - - - -
32C PHE* 3.0 3.5 + - - +
33C GLU* 2.9 69.4 + - - +
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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