Contacts of the helix formed by residues 13 - 32 (chain C) in PDB entry 5T5W
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 13 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A SER 4.8 2.6 + - - -
81A LYS* 4.7 6.7 - - - +
82A TYR* 3.1 18.9 + - - -
139A GLU* 3.2 22.7 + - - -
143A TRP* 3.4 25.5 - - - -
12C LEU* 1.3 73.7 - - - +
14C PRO* 1.3 68.0 - - - +
15C ARG* 4.4 1.0 - - - +
16C GLU* 3.0 30.5 + - - +
17C LEU* 3.2 10.0 + - - +
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Residues in contact with PRO 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.3 18.6 - - - +
140A TYR* 4.0 16.8 - - + -
143A TRP* 3.7 23.8 - - + -
183B THR* 3.8 25.8 - - + -
184B PHE 3.5 16.2 - - - +
185B SER 3.2 21.9 - - - +
12C LEU 3.7 3.4 - - - +
13C SER* 1.3 82.7 - - - +
15C ARG* 1.3 55.0 + - - +
17C LEU* 3.0 3.5 + - + +
18C GLN* 2.8 33.2 + - - +
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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
----------------------------------------------------------
81A LYS* 5.9 1.3 - - - +
137A GLU 5.5 0.4 + - - -
138A ASN* 2.6 41.4 + - + +
139A GLU* 3.4 21.6 + - - +
140A TYR* 3.5 28.4 + - - -
13C SER* 3.2 1.5 - - - +
14C PRO* 1.3 76.6 - - - +
16C GLU* 1.3 62.5 + - - +
18C GLN* 3.1 29.4 + - - +
19C ALA* 3.1 21.1 + - - +
22C ARG* 4.8 2.7 + - - +
88C GLN* 5.1 4.5 + - - +
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 2.7 38.3 + - - +
82A TYR* 3.5 12.4 - - + -
12C LEU* 5.2 4.3 - - + -
13C SER* 3.0 23.2 + - - +
15C ARG* 1.3 79.4 - - - +
17C LEU* 1.3 58.9 + - + +
19C ALA* 3.1 7.1 + - - +
20C PHE* 2.9 51.1 + - + -
88C GLN* 3.0 35.3 + - - +
89C PRO 4.9 0.2 - - - -
92C THR* 3.0 22.1 + - + +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.2 63.9 - - + +
185B SER* 4.0 14.0 - - - -
12C LEU* 4.0 43.1 - - + +
13C SER 3.2 7.9 + - - +
14C PRO 3.0 7.4 + - - +
16C GLU* 1.3 72.4 - - - +
18C GLN* 1.3 55.4 + - - +
20C PHE* 3.2 15.5 + - + +
21C LYS* 2.7 35.5 + - - +
146C PHE* 4.3 9.4 - - + -
149C LEU* 4.5 5.4 - - + -
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Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 2.8 33.7 + - - -
185B SER* 2.9 30.9 + - - +
186B VAL* 3.4 11.0 - - + +
14C PRO 2.8 16.3 + - - +
15C ARG* 3.1 34.8 + - - +
17C LEU* 1.3 77.5 - - - +
19C ALA* 1.3 56.3 + - - +
21C LYS* 3.4 6.5 + - - +
22C ARG* 3.1 49.2 + - - +
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Residues in contact with ALA 19 (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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15C ARG 3.1 14.2 + - - +
16C GLU* 3.1 22.4 + - - +
18C GLN* 1.3 74.6 - - - +
20C PHE* 1.3 63.7 + - + +
22C ARG* 3.5 22.4 + - - +
23C ALA* 3.2 19.8 + - - +
85C VAL* 4.5 2.6 - - - +
88C GLN* 3.9 21.5 - - + +
89C PRO* 3.7 13.7 - - + +
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Residues in contact with PHE 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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12C LEU* 5.3 3.4 - - + -
16C GLU* 2.9 48.5 + - + -
17C LEU* 3.2 11.6 + - + +
19C ALA* 1.3 74.0 - - - +
21C LYS* 1.3 60.5 + - - +
23C ALA* 2.9 7.0 + - + +
24C LYS* 2.9 28.1 + - - +
89C PRO* 3.4 44.9 - - + -
92C THR* 4.0 12.6 - - + -
93C LEU* 3.8 29.6 - - + -
145C LEU* 4.3 16.5 - - + +
146C PHE* 3.9 18.1 - - + -
149C LEU* 3.7 27.4 - - + -
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Residues in contact with LYS 21 (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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98B ASP* 2.8 30.9 + - - +
101B PHE* 3.4 46.2 - - + -
185B SER* 5.3 0.4 - - - -
17C LEU 2.7 20.3 + - - +
18C GLN* 3.8 8.1 - - - +
19C ALA 3.3 0.2 - - - -
20C PHE* 1.3 72.0 - - - +
22C ARG* 1.3 57.8 + - + +
24C LYS* 3.4 6.8 + - + +
25C ASP* 3.0 64.3 + - - +
146C PHE* 3.6 11.6 - - + -
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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
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15C ARG* 4.8 3.2 + - - +
18C GLN* 3.1 44.4 + - - +
19C ALA* 3.5 29.0 + - - +
21C LYS* 1.3 76.8 - - + +
23C ALA* 1.3 57.7 + - - +
25C ASP* 3.7 7.4 + - - +
26C ALA* 3.1 27.5 + - - +
85C VAL* 3.5 20.3 - - + +
88C GLN* 5.3 2.4 + - - -
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Residues in contact with ALA 23 (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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19C ALA 3.2 12.9 + - - +
20C PHE* 2.9 11.3 + - - +
22C ARG* 1.3 75.4 - - - +
24C LYS* 1.3 61.4 + - - +
26C ALA* 2.9 3.6 + - - +
27C LEU* 2.8 36.7 + - + +
85C VAL* 3.5 11.6 - - + +
86C LEU* 3.6 25.6 - - + -
89C PRO* 4.0 15.3 - - + -
145C LEU* 5.0 5.6 - - + -
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TYR 3.3 18.4 + - - -
74B ASN* 2.8 34.2 + - - +
75B LYS 5.1 0.2 - - - +
98B ASP* 4.2 12.0 + - - -
101B PHE* 5.7 0.2 - - - -
20C PHE 2.9 14.8 + - - +
21C LYS* 4.0 9.9 - - - +
23C ALA* 1.3 76.1 - - - +
25C ASP* 1.3 64.3 + - - +
27C LEU* 4.0 2.8 - - - +
28C GLU* 3.1 51.9 + - - +
142C THR* 4.0 31.9 - - + +
143C PHE* 4.6 2.8 + - - +
145C LEU* 4.5 8.9 - - + +
146C PHE* 3.5 33.1 - - + +
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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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21C LYS* 3.0 57.5 + - - +
22C ARG* 4.0 7.6 - - - +
24C LYS* 1.3 78.6 - - - +
26C ALA* 1.3 58.1 + - - +
28C GLU* 3.8 13.5 + - - +
29C GLU* 3.2 33.1 + - - +
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Residues in contact with ALA 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 19.0 + - - +
23C ALA* 2.9 7.4 + - - +
25C ASP* 1.3 75.7 - - - +
27C LEU* 1.3 64.3 + - - +
29C GLU* 3.4 20.1 + - - +
30C SER* 3.5 7.6 + - - -
82C LEU* 3.5 30.2 - - + +
85C VAL* 4.4 14.6 - - + -
86C LEU* 6.2 0.7 - - + -
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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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23C ALA* 2.8 26.9 + - + +
24C LYS* 4.0 1.8 - - - +
26C ALA* 1.3 72.1 - - - +
28C GLU* 1.3 61.3 + - - +
30C SER* 3.0 4.8 + - - +
31C LEU* 2.9 29.7 + - - +
72C LEU* 3.8 24.2 - - + -
75C THR* 4.1 11.2 - - + -
82C LEU* 3.8 20.0 - - + -
86C LEU* 3.7 37.0 - - + -
138C GLU* 6.1 2.9 - - + -
142C THR* 3.4 38.1 - - + +
145C LEU* 5.1 4.9 - - + -
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Residues in contact with GLU 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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42B SER* 4.4 0.5 + - - -
74B ASN* 4.3 1.4 - - - +
75B LYS* 2.8 33.2 + - - +
24C LYS* 3.1 46.7 + - - +
25C ASP* 4.1 14.3 - - - +
27C LEU* 1.3 76.4 - - - +
29C GLU* 1.3 62.0 + - + +
31C LEU* 4.4 6.5 - - - -
32C LEU* 3.3 35.2 + - + +
142C THR* 4.3 7.4 - - + -
143C PHE* 3.6 28.0 - - + -
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Residues in contact with GLU 29 (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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25C ASP* 3.2 23.2 - - - +
26C ALA* 3.4 11.7 + - - +
27C LEU 3.1 0.8 - - - -
28C GLU* 1.3 79.5 - - + +
30C SER* 1.3 58.7 + - - +
32C LEU* 4.0 3.6 + - - +
33C LEU* 3.4 25.3 - - - +
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Residues in contact with SER 30 (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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26C ALA 3.5 2.7 + - - -
27C LEU* 3.0 6.1 + - - -
29C GLU* 1.3 79.2 - - - +
31C LEU* 1.3 61.8 + - - +
32C LEU 3.3 1.1 + - - -
33C LEU* 3.5 6.4 + - - +
34C LYS* 3.4 21.3 + - - +
79C ASP* 4.9 4.9 + - - +
82C LEU* 3.6 31.8 - - - +
138C GLU* 5.3 4.5 + - - -
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Residues in contact with LEU 31 (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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27C LEU 2.9 16.4 + - - +
28C GLU* 4.1 7.6 - - - +
29C GLU 3.5 0.4 - - - -
30C SER* 1.3 76.9 - - - +
32C LEU* 1.3 67.9 + - + +
34C LYS* 3.4 14.9 + - - +
36C CYS* 3.5 23.6 - - + +
135C GLY* 5.3 2.2 - - - +
138C GLU* 5.7 5.4 - - + -
139C ALA* 4.3 27.6 - - + +
142C THR* 5.9 2.7 - - + +
143C PHE* 5.5 6.3 - - + -
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.3 28.1 + - + +
29C GLU* 4.4 2.2 - - - +
30C SER 3.3 1.0 - - - -
31C LEU* 1.3 81.4 - - + +
33C LEU* 1.3 70.7 + - + +
34C LYS 3.7 4.5 + - - +
36C CYS* 5.1 4.3 - - - -
143C PHE* 5.6 8.5 - - + -
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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