Contacts of the helix formed by residues 6 - 19 (chain C) in PDB entry 5SY1
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 THR 6 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A THR* 6.0 6.5 - - + -
5C LEU* 1.3 81.0 - - - +
7C GLU* 1.3 72.3 + - - +
8C GLU* 3.6 8.1 + - - +
9C GLN* 3.4 34.1 + - - +
10C ILE* 3.3 23.2 + - - +
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Residues in contact with GLU 7 (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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6C THR* 1.3 80.7 - - - +
8C GLU* 1.3 61.1 + - + +
10C ILE* 3.4 5.8 + - - +
11C ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 8 (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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235A LYS* 5.0 8.5 + - - -
376A ARG* 4.0 35.3 + - - +
378A ASP* 6.1 1.8 - - + -
6C THR* 3.4 7.8 + - - +
7C GLU* 1.3 80.5 - - + +
9C GLN* 1.3 60.1 + - + +
11C ALA* 2.9 23.1 + - - +
12C GLU* 3.3 18.3 + - - +
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Residues in contact with GLN 9 (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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232A ILE* 3.6 40.2 + - + +
233A LEU 5.2 0.9 - - - +
235A LYS* 3.7 28.7 - - + +
236A LYS* 4.6 11.1 - - - +
239A THR* 4.9 3.4 + - - -
4C GLN 4.8 0.3 - - - +
5C LEU* 3.3 42.1 - - + +
6C THR* 3.4 24.3 + - - +
7C GLU 3.4 0.8 - - - -
8C GLU* 1.3 78.6 - - + +
10C ILE* 1.3 60.6 + - - +
12C GLU* 4.2 6.6 + - - +
13C PHE* 3.5 26.3 + - - -
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Residues in contact with ILE 10 (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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619A ASN* 4.2 16.6 - - + +
621A SER* 5.7 3.8 - - - +
622A LEU* 4.2 31.9 - - + -
5C LEU* 3.6 36.1 - - + +
6C THR 3.3 19.7 + - - +
7C GLU* 3.4 5.1 + - - +
8C GLU 3.2 0.4 - - - -
9C GLN* 1.3 76.1 - - - +
11C ALA* 1.3 60.0 + - - +
12C GLU 3.2 0.7 - - - -
13C PHE* 3.4 6.6 + - + +
14C LYS* 2.9 30.1 + - + +
66C PHE* 4.4 13.0 - - + -
70C LEU* 5.5 3.6 - - + -
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Residues in contact with ALA 11 (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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376A ARG* 3.8 22.3 - - + +
7C GLU 2.9 17.8 + - - +
8C GLU* 2.9 11.6 + - + +
10C ILE* 1.3 77.7 - - - +
12C GLU* 1.3 57.4 + - - +
14C LYS* 3.4 9.2 - - - +
15C GLU* 3.0 24.8 + - - +
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Residues in contact with GLU 12 (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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228A TYR* 4.2 14.6 + - - -
232A ILE* 3.4 34.3 - - - +
372A LYS 4.7 0.9 - - - +
375A TYR* 4.1 12.3 - - - +
376A ARG* 3.2 46.8 + - + +
557A HIS* 5.0 8.6 - - + -
559A VAL* 4.7 4.1 - - + +
8C GLU 3.3 9.3 + - - +
9C GLN* 4.2 4.9 + - - +
10C ILE 3.2 0.6 - - - -
11C ALA* 1.3 76.3 - - - +
13C PHE* 1.3 66.2 + - + +
15C GLU* 2.8 9.7 + - - +
16C ALA* 2.8 29.9 + - - +
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Residues in contact with PHE 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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229A VAL* 4.5 16.2 - - + -
232A ILE* 4.1 34.3 - - + -
233A LEU* 5.9 7.0 - - + -
559A VAL* 3.6 31.4 - - + -
5C LEU* 4.9 8.1 - - + -
9C GLN 3.5 19.3 - - - -
10C ILE* 3.4 8.4 + - - +
12C GLU* 1.3 76.0 - - + +
14C LYS* 1.3 64.2 + - - +
16C ALA* 4.4 2.0 - - - +
17C PHE* 3.1 18.4 + - - +
66C PHE* 3.2 25.0 - - + -
69C PHE* 3.9 14.4 - + + -
70C LEU* 3.5 29.6 - - + -
73C MET* 4.9 13.0 - - + -
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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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622A LEU* 5.4 2.6 - - - +
625A SER* 4.7 15.8 + - - -
629A PHE* 5.1 11.9 - - - -
10C ILE* 2.9 21.7 + - + +
11C ALA* 3.4 9.6 - - - +
13C PHE* 1.3 78.6 - - - +
15C GLU* 1.3 60.4 + - - +
17C PHE* 3.7 7.6 + - + +
18C SER* 3.4 19.6 + - - -
66C PHE* 3.6 42.8 - - + +
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Residues in contact with GLU 15 (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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374A LEU 5.1 3.4 - - - +
375A TYR 3.6 23.1 - - - +
376A ARG 4.7 2.6 - - - +
377A GLY* 4.9 10.8 - - - +
389A ILE* 4.0 22.9 - - - +
553A VAL* 6.1 1.1 - - + -
557A HIS* 4.8 11.4 - - + +
11C ALA 3.0 12.7 + - - +
12C GLU 2.8 10.1 + - - +
14C LYS* 1.3 76.1 - - - +
16C ALA* 1.3 59.6 + - - +
18C SER* 2.3 44.5 + - - -
19C LEU* 3.5 17.1 + - + +
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Residues in contact with ALA 16 (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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557A HIS* 4.4 8.7 - - + +
559A VAL* 4.0 31.6 - - + -
560A MET* 4.2 14.2 - - + +
12C GLU 2.8 17.4 + - - +
13C PHE* 4.4 2.9 - - - +
15C GLU* 1.3 74.2 - - - +
17C PHE* 1.3 60.2 + - - +
19C LEU* 3.5 19.0 + - - +
20C PHE* 3.4 21.0 - - - -
69C PHE* 4.9 4.9 - - + -
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Residues in contact with PHE 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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13C PHE 3.1 20.3 + - - +
14C LYS* 3.8 9.6 - - + +
16C ALA* 1.3 77.6 - - - +
18C SER* 1.3 65.3 - - - +
20C PHE* 3.2 17.7 + - - +
21C ASP* 3.6 13.9 + - + +
26C GLY* 3.5 41.7 - - - -
27C THR* 4.0 5.6 - - - -
28C ILE* 3.6 33.4 - - + -
64C ILE* 4.1 3.1 - - + -
65C ASP 4.2 7.0 - - - -
66C PHE* 3.8 25.8 - + + -
69C PHE* 3.9 36.0 - + + -
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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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14C LYS 3.4 10.3 + - - -
15C GLU* 2.3 40.7 + - - -
17C PHE* 1.3 82.4 - - - +
19C LEU* 1.3 64.0 + - - +
20C PHE 3.1 1.1 + - - -
21C ASP* 3.5 20.3 - - - +
22C LYS* 5.2 3.8 + - - +
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Residues in contact with LEU 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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389A ILE* 4.8 10.1 - - + -
553A VAL 3.9 19.3 - - - +
554A SER* 4.4 22.0 - - - +
557A HIS* 4.0 16.4 - - + -
560A MET* 3.9 33.0 - - + +
15C GLU* 3.5 19.2 + - - +
16C ALA* 3.8 15.3 - - - +
17C PHE 3.2 1.0 - - - -
18C SER* 1.3 83.4 - - - +
20C PHE* 1.3 62.3 + - - +
22C LYS* 4.1 23.7 + - - +
36C VAL* 4.4 9.4 - - - +
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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
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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