Contacts of the helix formed by residues 17 - 30 (chain A) in PDB entry 1CCW
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 ALA 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A CYS 3.7 8.5 - - - +
16A HIS* 1.3 73.2 - - - +
18A VAL* 1.3 67.0 + - - +
19A GLY 3.4 2.0 - - - -
20A ASN* 3.3 8.0 + - - +
21A LYS* 3.2 32.0 + - + +
39A VAL* 3.9 15.0 - - + -
800A CNC 2.8 13.1 + - - +
408B PHE* 3.9 20.4 - - + +
410B PRO* 4.4 10.3 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 5.3 0.2 - - - +
17A ALA* 1.3 78.8 - - - +
19A GLY* 1.3 63.4 + - - +
21A LYS* 3.1 9.1 + - + +
22A ILE* 3.1 22.7 + - + +
800A CNC 3.6 34.3 + - + +
220B THR* 5.1 0.7 - - - +
222B THR* 3.6 25.6 - - + +
408B PHE* 3.8 30.7 - - + -
470B ILE* 3.9 40.2 - - + -
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A HIS* 5.4 0.8 - - - +
17A ALA 3.4 0.6 - - - +
18A VAL* 1.3 78.6 - - - +
20A ASN* 1.3 51.7 + - - +
22A ILE* 3.2 2.0 + - - +
23A LEU* 2.8 44.8 + - - +
63A LEU* 5.6 4.1 - - - +
800A CNC 3.7 46.6 + - - -
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 16.6 - - - +
9A GLY* 4.1 12.5 - - - -
10A VAL* 4.0 22.3 - - + +
16A HIS 5.2 1.0 + - - -
17A ALA* 3.3 14.3 + - - +
19A GLY* 1.3 77.8 - - - +
21A LYS* 1.3 79.8 + - - +
23A LEU* 3.5 8.0 + - - +
24A ASP* 3.0 23.6 + - - +
36A ASN* 2.9 40.9 + - - +
38A GLY* 4.2 9.8 - - - -
39A VAL* 5.0 2.8 - - + +
61A SER* 6.1 1.1 - - - -
63A LEU* 5.7 2.2 - - - +
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Residues in contact with LYS 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 ALA* 3.2 18.7 + - + +
18A VAL* 3.1 10.8 + - + +
20A ASN* 1.3 94.6 + - - +
22A ILE* 1.3 61.2 + - + +
24A ASP* 3.4 5.7 + - + +
25A HIS* 3.0 28.2 + - - +
36A ASN* 4.2 10.0 - - - +
38A GLY* 5.7 3.6 - - - -
408B PHE* 4.9 20.2 - - + -
463B PHE* 6.1 5.4 - - + -
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Residues in contact with ILE 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 VAL* 3.1 16.2 + - + +
19A GLY 3.2 5.1 + - - +
21A LYS* 1.3 75.4 - - + +
23A LEU* 1.3 61.6 + - - +
25A HIS* 3.3 8.6 + - + +
26A ALA* 2.8 30.1 + - + +
123A PRO* 4.3 9.4 - - + -
800A CNC 3.7 38.4 - - + +
408B PHE* 6.3 1.1 - - + -
463B PHE* 5.4 6.1 - - + -
467B ILE* 4.1 34.5 - - + -
470B ILE* 4.6 14.1 - - + -
471B PHE* 3.8 17.5 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.9 31.6 - - + -
19A GLY 2.8 26.5 + - - +
20A ASN* 4.6 2.5 - - - -
22A ILE* 1.3 73.4 - - - +
24A ASP* 1.3 62.8 + - - +
26A ALA* 4.5 2.2 - - - +
27A PHE* 2.9 54.3 + - + +
59A LEU* 5.8 0.4 - - + -
61A SER* 4.7 5.2 - - - +
123A PRO* 4.0 13.9 - - + -
800A CNC 3.7 65.7 - - + +
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Residues in contact with ASP 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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8A LEU* 3.7 8.4 - - + +
20A ASN 3.0 17.9 + - - +
21A LYS* 3.7 8.3 + - + +
23A LEU* 1.3 74.4 - - - +
25A HIS* 1.3 64.1 + - - +
28A THR* 2.8 43.7 + - - -
34A VAL* 3.7 20.0 - - - +
36A ASN* 2.9 31.4 + - - +
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Residues in contact with HIS 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 LYS 3.0 18.8 + - - +
22A ILE* 3.5 11.2 - - + +
24A ASP* 1.3 78.0 + - - +
26A ALA* 1.3 62.6 + - + +
28A THR* 3.8 3.8 - - - -
29A ASN* 2.9 61.9 + - - +
463B PHE* 4.4 18.8 - + + -
464B GLN* 4.5 8.5 + - - -
467B ILE* 3.5 33.1 - - + +
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Residues in contact with ALA 26 (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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22A ILE* 2.8 21.9 + - + +
23A LEU 3.9 1.6 - - - +
25A HIS* 1.3 80.8 - - + +
27A PHE* 1.3 58.5 + - + +
29A ASN* 3.3 6.5 + - - +
30A ALA* 3.0 26.5 + - - +
123A PRO* 3.7 28.9 - - + -
124A GLU* 4.5 7.9 - - - +
127A ILE* 3.8 11.5 - - + +
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Residues in contact with PHE 27 (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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6A ILE* 3.9 15.3 - - + -
8A LEU* 6.1 0.7 - - + -
23A LEU* 2.9 49.4 + - + +
26A ALA* 1.3 75.4 - - + +
28A THR* 1.3 66.8 + - - +
30A ALA* 3.3 9.6 + - - -
31A GLY 3.3 0.3 + - - -
32A PHE* 3.1 40.2 + + + +
34A VAL* 3.8 17.9 - - + -
59A LEU* 3.5 27.6 - - + -
123A PRO* 3.9 8.3 - - + -
126A GLY* 3.7 9.4 - - - -
127A ILE* 3.7 44.6 - - + -
130A LEU* 4.0 15.3 - - + -
800A CNC 5.0 2.0 - - + -
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Residues in contact with THR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASP* 2.8 37.6 + - - -
25A HIS* 3.8 4.7 - - - -
27A PHE* 1.3 77.8 - - - +
29A ASN* 1.3 65.0 + - - +
31A GLY* 2.9 20.3 + - - -
32A PHE 3.6 14.0 + - - +
34A VAL* 3.5 11.3 + - - +
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Residues in contact with ASN 29 (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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25A HIS* 2.9 52.2 + - - +
26A ALA* 3.5 6.9 - - - +
28A THR* 1.3 82.6 - - - +
30A ALA* 1.3 60.8 + - - +
31A GLY 3.4 0.5 + - - -
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Residues in contact with ALA 30 (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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1A MET* 3.6 26.3 + - - +
26A ALA 3.0 12.7 + - - +
27A PHE 3.6 9.0 - - - +
28A THR 3.1 0.6 - - - -
29A ASN* 1.3 76.0 - - - +
31A GLY* 1.3 57.4 + - - +
32A PHE* 3.6 9.0 - - + -
127A ILE* 3.9 31.6 - - + -
131A LYS* 4.6 5.7 - - - +
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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