Contacts of the helix formed by residues 22 - 30 (chain B) 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 GLN 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLU* 3.1 25.2 + - - +
19B GLU* 3.2 15.5 + - - +
20B VAL 3.1 1.2 + - - -
21B LEU* 1.3 78.2 - - + +
23B GLN* 1.3 63.0 + - - +
24B TRP* 3.2 6.3 + - - +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 3.9 8.4 - - - +
20B VAL* 3.0 33.0 + - - +
21B LEU 3.2 0.2 - - - -
22B GLN* 1.3 77.1 - - - +
24B TRP* 1.3 70.8 + - - +
102B ASN* 5.4 3.6 - - - +
104B TYR* 4.1 14.4 + - + -
154B ASP* 4.6 8.8 + - - -
156B ARG* 3.3 27.1 + - - +
157B LEU* 3.9 26.0 - - + +
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Residues in contact with TRP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU 3.4 9.4 - - - +
22B GLN 3.2 4.5 - - - -
23B GLN* 1.3 82.9 - - - +
25B PRO* 1.3 81.6 - - + +
26B THR* 3.2 23.5 - - + +
27B GLY* 2.9 18.7 + - - -
104B TYR* 3.5 46.4 - + + -
105B ASP* 3.9 12.6 - - + -
108B GLU* 4.7 10.2 + - + -
128B VAL* 3.9 15.9 - - + -
129B ASN* 3.8 25.4 - - - +
157B LEU* 3.8 19.9 - - + +
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TRP* 1.3 111.8 - - + +
26B THR* 1.3 60.8 + - + +
27B GLY 3.1 1.5 + - - -
28B LYS* 3.2 28.7 + - + +
29B GLU* 4.6 1.2 + - - +
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TRP* 3.2 16.0 - - + +
25B PRO* 1.3 78.2 - - + +
27B GLY* 1.3 61.8 + - - +
28B LYS 3.0 0.4 - - - -
29B GLU* 3.0 36.8 + - - +
30B VAL* 4.2 5.4 + - - +
128B VAL* 2.8 30.7 + - - +
129B ASN 3.7 15.5 - - - +
130B PHE 4.7 0.2 - - - -
131B GLY* 3.8 17.7 - - - -
132B VAL* 4.8 0.3 - - - +
161B ILE* 3.4 14.2 - - - +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.3 40.4 - - - +
24B TRP 2.9 8.4 + - - -
26B THR* 1.3 78.2 + - - +
28B LYS* 1.3 60.2 + - - +
30B VAL* 3.2 24.5 + - - +
157B LEU* 4.2 16.0 - - - +
161B ILE* 4.7 0.6 - - - +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU 5.6 2.5 - - - +
24B TRP 5.7 0.2 - - - +
25B PRO* 3.2 20.4 + - + +
26B THR 3.0 0.6 - - - -
27B GLY* 1.3 77.4 - - - +
29B GLU* 1.3 60.2 + - + +
30B VAL 3.2 5.9 + - - +
31B ASP* 6.0 0.3 - - - +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO 5.1 0.9 - - - +
26B THR* 3.0 35.6 + - - +
28B LYS* 1.3 78.6 - - + +
30B VAL* 1.3 61.7 + - - +
31B ASP* 3.6 4.8 + - - +
34B GLU* 5.4 3.1 - - - +
130B PHE 4.5 1.0 - - - +
131B GLY* 3.5 2.8 - - - -
132B VAL* 2.9 50.3 + - + +
133B LYS* 3.0 22.0 + - - +
164B ALA* 5.4 0.2 - - - +
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.7 12.7 + - - +
21B LEU* 3.8 21.6 - - + +
26B THR 4.4 0.2 - - - +
27B GLY 3.6 18.4 - - - +
28B LYS 3.2 5.6 - - - +
29B GLU* 1.3 77.1 - - - +
31B ASP* 1.3 64.0 + - - +
32B LEU* 4.3 4.2 + - + +
132B VAL* 3.8 20.4 - - + -
160B GLU* 3.5 35.0 - - - +
161B ILE* 4.2 14.8 - - + -
164B ALA* 4.1 15.7 - - + -
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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