Contacts of the helix formed by residues 17 - 28 (chain B) in PDB entry 2C8U
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.0 16.8 - - + -
10B TYR* 3.8 38.4 - - + -
12B ASN 4.8 2.7 - - - +
15B GLY* 3.1 2.0 - - - -
16B ARG* 1.3 78.6 - - - +
18B GLU* 1.3 63.9 + - - +
19B SER 3.2 0.7 - - - -
20B ILE* 3.0 11.1 + - - +
21B GLN* 2.9 31.0 + - - +
54B PRO* 3.6 10.5 - - + +
1206B SO4 4.5 0.2 + - - -
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Residues in contact with GLU 18 (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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13B GLY 3.6 17.4 - - - +
14B ARG* 3.4 36.5 - - - +
15B GLY 3.5 10.9 - - - +
16B ARG 3.2 1.4 - - - -
17B ALA* 1.3 77.2 - - - +
19B SER* 1.3 58.3 + - - +
21B GLN* 3.6 12.2 + - - +
22B MET* 2.9 51.4 + - + +
165B ALA* 3.7 29.6 - - + +
168B ASP* 5.9 2.1 - - - +
169B HIS* 3.7 10.2 + - - -
202B TYR* 4.9 3.8 - - - +
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Residues in contact with SER 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 3.8 7.8 + - - -
17B ALA 3.2 0.8 - - - -
18B GLU* 1.3 79.9 - - - +
20B ILE* 1.3 55.6 + - - +
22B MET* 4.3 5.2 - - - +
23B THR* 2.6 34.7 + - - -
71B SER 5.7 0.4 - - - -
72B LEU* 3.8 26.2 - - - +
75B ALA* 3.9 6.8 - - - +
158B LEU* 4.5 2.1 - - - +
161B LEU* 4.7 3.0 + - - +
162B VAL* 3.8 27.8 - - - +
165B ALA* 4.5 9.0 - - - +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.0 27.4 - - + -
16B ARG 4.4 0.7 - - - +
17B ALA* 3.0 11.6 + - - +
19B SER* 1.3 74.8 - - - +
21B GLN* 1.3 65.4 + - - +
23B THR* 3.4 3.9 + - - -
24B LEU* 3.1 32.2 + - + +
54B PRO* 4.4 14.8 - - + -
56B VAL* 4.0 15.3 - - + -
71B SER* 3.6 46.2 - - - +
74B ILE* 4.0 28.9 - - + -
75B ALA* 4.4 6.3 - - + +
78B MET* 5.5 4.0 - - + +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.4 8.5 - - + -
10B TYR* 3.3 31.7 + - - -
13B GLY* 4.7 5.4 + - - +
17B ALA* 2.9 19.9 + - - +
18B GLU* 3.6 19.2 + - - +
20B ILE* 1.3 76.7 - - - +
22B MET* 1.3 57.2 + - - +
24B LEU* 3.3 4.2 + - - +
25B VAL* 2.8 33.7 + - - +
31B TYR* 3.6 23.9 + - + +
33B ASP* 3.0 32.7 + - - +
202B TYR* 3.2 22.8 + - - +
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 2.9 44.7 + - + +
19B SER* 4.3 0.9 - - - +
21B GLN* 1.3 69.3 - - - +
23B THR* 1.3 59.3 + - - +
25B VAL* 3.8 6.7 - - - +
26B ALA* 2.9 32.2 + - - +
161B LEU* 3.6 31.7 - - + +
164B ILE* 3.6 29.8 - - + -
165B ALA* 4.6 11.0 - - + -
168B ASP* 5.8 2.9 - - - +
199B LEU* 3.7 16.2 - - + +
202B TYR* 3.8 16.4 - - + +
203B LEU* 3.8 24.5 - - + -
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Residues in contact with THR 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 SER 2.6 24.5 + - - -
20B ILE* 3.7 5.6 - - - -
22B MET* 1.3 76.2 - - - +
24B LEU* 1.3 58.0 + - - +
26B ALA* 3.4 1.9 + - - +
27B ALA* 2.8 32.1 + - + +
75B ALA* 3.8 8.1 - - - +
78B MET* 3.9 11.9 - - + +
79B ALA* 3.6 38.6 - - + +
84B MET* 3.9 12.1 - - + +
158B LEU* 3.5 20.4 - - - +
161B LEU* 3.5 10.9 - - + +
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Residues in contact with LEU 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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6B ILE* 4.1 17.7 - - + -
8B VAL* 4.1 11.0 - - + -
20B ILE* 3.1 27.3 + - + +
21B GLN 3.7 1.3 - - - +
23B THR* 1.3 76.1 - - - +
25B VAL* 1.3 61.7 + - - +
27B ALA* 3.2 3.8 + - + +
28B GLY 3.0 4.7 + - - -
29B VAL* 2.9 53.9 + - + +
31B TYR* 3.6 45.5 - - + -
78B MET* 4.0 35.2 - - + -
82B HIS* 5.8 1.6 - - + +
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Residues in contact with VAL 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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21B GLN 2.8 23.9 + - - +
22B MET* 3.8 6.7 - - - +
23B THR 3.4 0.2 - - - -
24B LEU* 1.3 72.1 - - - +
26B ALA* 1.3 58.1 + - - +
28B GLY* 3.0 17.2 + - - -
29B VAL 4.9 2.2 - - - +
31B TYR* 3.5 23.6 - - + +
198B ARG* 3.2 48.0 - - + +
199B LEU* 3.8 7.6 - - + +
202B TYR* 3.6 30.1 - - + -
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Residues in contact with ALA 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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22B MET 2.9 20.8 + - - +
23B THR 3.8 2.7 - - - +
25B VAL* 1.3 75.1 - - - +
27B ALA* 1.3 53.7 + - - +
28B GLY 3.1 0.2 - - - -
84B MET* 4.1 17.9 - - - +
156B VAL* 4.3 15.0 - - + -
161B LEU* 4.3 7.6 - - + -
196B SER* 4.0 21.4 + - - +
198B ARG* 2.7 27.2 + - - +
199B LEU* 5.2 3.4 - - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 2.8 19.6 + - + +
24B LEU* 3.2 3.3 + - + +
26B ALA* 1.3 76.2 - - - +
28B GLY* 1.3 61.3 + - - +
29B VAL* 3.6 22.3 + - + +
78B MET 5.3 0.2 - - - +
82B HIS* 3.7 24.6 + - + -
84B MET* 3.7 19.0 - - + +
198B ARG* 3.5 7.2 + - - +
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Residues in contact with GLY 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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25B VAL 3.0 16.1 + - - -
26B ALA 3.1 1.8 + - - -
27B ALA* 1.3 78.4 - - - +
29B VAL* 1.3 58.6 + - - +
30B ASN* 4.1 3.6 + - - +
198B ARG* 3.6 23.1 - - - -
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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