Contacts of the helix formed by residues 5 - 29 (chain A) in PDB entry 4CSC
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 ASN 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER 4.1 2.6 + - - +
4A THR* 1.3 81.0 - - - +
6A LEU* 1.3 65.8 + - - +
7A LYS* 2.8 38.4 - - - +
8A ASP* 3.0 39.2 + - + +
9A VAL* 3.3 16.3 + - - +
109A TRP* 4.0 16.0 - - - -
172A TYR* 4.1 2.0 + - - -
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 1.3 74.8 - - - +
7A LYS* 1.3 63.3 + - - +
9A VAL* 3.2 5.0 + - + -
10A LEU* 3.1 22.5 + - + +
93A PHE* 3.8 28.7 - - + -
94A TRP* 3.8 26.7 - - + -
97A VAL* 3.9 20.0 - - + -
98A THR* 3.4 33.2 - - + -
109A TRP* 3.5 25.4 - - + -
110A LEU* 4.4 7.9 - - + -
172A TYR* 3.7 22.9 - - + +
176A MET* 4.9 0.9 - - - -
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 2.8 18.7 - - - +
6A LEU* 1.3 80.7 - - - +
8A ASP* 1.3 55.7 + - - +
10A LEU* 3.5 4.4 + - - +
11A ALA* 3.1 27.2 + - - +
168A TRP* 3.6 19.8 - - + -
169A GLU* 3.4 47.7 + - - +
172A TYR* 3.6 23.3 + - + -
173A GLU* 2.9 29.5 + - - +
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN* 3.0 32.2 + - + +
7A LYS* 1.3 74.0 - - - +
9A VAL* 1.3 68.9 + - + +
11A ALA* 3.4 8.9 + - - +
12A ALA* 3.2 19.2 + - - +
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASN 3.3 12.5 + - - +
6A LEU* 3.2 9.3 + - + +
8A ASP* 1.3 78.3 - - + +
10A LEU* 1.3 55.5 + - - +
12A ALA* 2.8 28.4 + - - +
13A LEU* 3.0 32.1 + - + +
94A TRP* 4.3 20.0 - - + +
98A THR* 4.0 17.3 - - + -
100A GLN* 5.2 7.0 - - - +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.1 10.5 + - + +
7A LYS* 3.6 7.6 - - - +
8A ASP 3.3 0.2 - - - -
9A VAL* 1.3 81.7 - - + +
11A ALA* 1.4 53.5 + - - +
13A LEU* 3.1 8.5 + - + +
14A ILE* 2.8 43.9 + - + +
97A VAL* 3.5 35.0 - - + +
168A TRP* 3.8 17.9 - - + -
172A TYR* 3.7 33.4 - - + -
410A ILE* 4.2 13.2 - - + -
411A TRP* 3.7 32.5 - - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS 3.1 14.5 + - - +
8A ASP* 3.6 13.9 - - - +
10A LEU* 1.4 73.9 - - - +
12A ALA* 1.3 58.2 + - - +
14A ILE* 4.7 2.2 - - - -
15A PRO* 3.1 24.9 - - - +
168A TRP* 4.2 17.4 - - + -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP 3.2 8.4 + - - +
9A VAL* 2.8 14.7 + - - +
11A ALA* 1.3 79.5 - - - +
13A LEU* 1.4 57.7 + - - +
15A PRO* 3.2 15.8 - - - +
16A LYS* 3.9 15.7 - - - +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.0 31.5 + - + +
10A LEU* 3.5 10.8 - - + +
12A ALA* 1.4 72.4 - - - +
14A ILE* 1.4 63.5 + - - +
16A LYS* 3.0 23.0 + - - +
17A GLU* 3.2 18.5 + - + +
97A VAL 4.8 0.2 - - - +
98A THR* 3.6 37.2 - - + +
100A GLN* 4.8 8.1 - - - +
411A TRP* 3.6 33.0 - - + -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 2.8 32.5 + - + +
11A ALA* 4.7 1.8 - - - +
13A LEU* 1.4 67.9 - - - +
15A PRO* 1.3 65.6 - - + +
17A GLU* 3.3 3.3 + - - +
18A GLN* 2.9 58.1 + - + +
168A TRP* 3.3 57.7 - - + +
410A ILE* 5.6 0.4 - - + -
411A TRP* 4.0 17.5 - - + -
414A ALA* 3.4 29.6 - - + +
415A LEU* 4.8 0.8 - - + +
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Residues in contact with PRO 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 3.1 23.3 - - - +
12A ALA* 3.2 13.2 - - - +
14A ILE* 1.3 96.0 - - + +
16A LYS* 1.3 61.7 + - + +
18A GLN* 3.2 18.6 - - - +
19A ALA* 3.1 23.6 + - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA 3.9 17.7 - - - +
13A LEU* 3.0 10.4 + - - +
15A PRO* 1.3 77.9 - - + +
17A GLU* 1.3 60.1 + - - +
19A ALA* 3.3 6.0 + - - +
20A ARG* 2.9 30.3 + - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.2 11.1 + - + +
14A ILE 3.7 7.2 - - - +
16A LYS* 1.3 81.1 - - - +
18A GLN* 1.3 54.9 - - - +
20A ARG* 2.7 48.8 + - - +
21A ILE* 2.8 50.9 + - + +
54A GLU* 5.0 4.3 - - - +
411A TRP* 3.8 30.1 - - + -
415A LEU* 4.1 13.7 - - + -
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 2.9 33.0 + - + +
15A PRO* 3.2 22.9 - - - +
17A GLU* 1.3 78.8 - - - +
19A ALA* 1.3 57.5 + - - +
21A ILE* 3.5 3.2 + - - +
22A LYS* 3.0 29.1 + - - +
414A ALA 3.4 22.7 + - - +
415A LEU* 4.4 13.3 - - + +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PRO 3.1 13.4 + - - +
16A LYS* 3.6 5.4 - - - +
18A GLN* 1.3 77.3 - - - +
20A ARG* 1.3 63.7 + - - +
22A LYS* 3.0 20.4 + - - +
23A THR* 3.2 19.6 + - - -
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Residues in contact with ARG 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS 2.9 18.4 + - - +
17A GLU* 2.7 36.3 + - - +
19A ALA* 1.3 77.5 - - - +
21A ILE* 1.4 63.6 + - + +
23A THR* 3.9 4.4 + - - -
24A PHE* 3.4 20.7 + - + +
54A GLU* 6.3 0.8 - - - +
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 2.8 29.8 + - - +
18A GLN* 4.0 4.0 - - - +
20A ARG* 1.4 70.5 - - + +
22A LYS* 1.3 65.7 + - + +
24A PHE* 3.3 10.0 + - + +
25A ARG* 3.1 46.0 + - + +
52A VAL* 5.8 1.1 - - + -
54A GLU* 4.0 14.1 - - - +
415A LEU* 3.8 40.6 - - + -
417A PHE* 4.9 9.6 - - + -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLN 3.0 14.2 + - - +
19A ALA* 3.0 19.1 + - - +
21A ILE* 1.3 75.3 - - + +
23A THR* 1.3 57.3 + - - +
25A ARG* 3.0 8.8 + - + +
26A GLN* 2.8 50.9 + - - +
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Residues in contact with THR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 3.2 15.9 + - - -
20A ARG* 4.3 4.1 + - - -
22A LYS* 1.3 78.2 - - - +
24A PHE* 1.3 62.6 + - - +
26A GLN* 3.1 17.2 + - + +
27A GLN* 3.0 32.6 + - + +
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG 3.4 16.9 + - - +
21A ILE* 3.3 10.5 + - + +
22A LYS 3.1 1.0 - - - -
23A THR* 1.3 80.6 - - - +
25A ARG* 1.3 72.9 + - + +
27A GLN* 3.8 9.6 - - - +
28A HIS* 2.9 58.0 + + + +
33A LEU* 6.2 3.8 - - + -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.1 37.8 + - + +
22A LYS* 3.0 7.9 + - + +
24A PHE* 1.3 90.7 - - + +
26A GLN* 1.3 62.4 + - - +
29A GLY* 2.8 36.3 + - - +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 2.8 37.6 + - - +
23A THR* 3.5 18.9 - - + +
24A PHE 3.1 0.2 - - - -
25A ARG* 1.3 79.2 - - - +
27A GLN* 1.3 57.9 + - - +
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Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A THR* 3.0 25.2 + - + +
24A PHE* 3.8 11.4 - - - +
26A GLN* 1.3 81.7 - - - +
28A HIS* 1.3 86.1 + - + +
29A GLY 3.9 0.2 - - - -
31A THR* 4.8 0.5 + - - -
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Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 2.9 44.9 + + + +
25A ARG* 4.7 0.4 - - - -
27A GLN* 1.3 111.4 + - + +
29A GLY* 1.3 62.6 + - - +
30A GLY 3.0 3.8 - - - +
31A THR* 2.8 53.7 + - + +
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Residues in contact with GLY 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 2.8 30.4 + - - +
27A GLN 3.9 0.6 - - - -
28A HIS* 1.3 77.7 - - - +
30A GLY* 1.3 58.1 + - - +
31A THR 3.6 4.3 + - - +
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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
------------------------------------------------------------
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