Contacts of the helix formed by residues 20 - 30 (chain B) in PDB entry 3IEU
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 GLY 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ASN 3.1 3.0 - - - -
19B VAL* 1.3 79.2 - - - +
21B LYS* 1.3 64.6 + - - +
23B THR* 3.1 3.1 + - - -
24B LEU* 2.9 24.9 + - - +
95B VAL* 4.8 3.1 - - - -
124B ASN* 3.6 10.3 - - - -
156B ALA* 4.3 2.3 - - - +
302B GDP 2.9 35.5 + - - -
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Residues in contact with LYS 21 (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 ILE* 3.9 28.3 - - + +
14B VAL* 3.6 24.2 - - - +
15B GLY 2.7 28.6 + - - +
16B ARG 3.1 13.3 + - - -
17B PRO* 3.6 4.4 - - - +
19B VAL* 3.7 12.7 - - + +
20B GLY* 1.3 71.0 - - - +
22B SER* 1.3 56.9 + - - +
24B LEU* 3.2 5.4 + - - +
25B LEU* 2.8 29.8 + - - +
62B ASP* 6.3 2.2 - - - -
95B VAL* 4.4 4.5 - - + +
302B GDP 2.8 41.5 + - - +
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Residues in contact with SER 22 (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 LYS* 1.3 74.2 - - - +
23B THR* 1.3 57.9 + - - +
25B LEU* 3.4 11.0 + - - +
26B ASN* 3.0 36.6 + - - -
36B THR* 5.8 8.1 - - - -
302B GDP 2.6 35.1 + - - -
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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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20B GLY 3.4 7.0 - - - -
22B SER* 1.3 78.7 - - - +
24B LEU* 1.3 60.0 + - - +
26B ASN* 3.4 8.5 + - + +
27B LYS* 3.2 22.2 + - + +
36B THR* 6.3 1.6 - - - -
156B ALA* 3.6 26.0 - - + +
157B GLU* 4.2 6.3 - - + +
302B GDP 2.9 52.4 + - + +
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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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13B ILE* 4.5 10.1 - - + -
20B GLY 2.9 15.3 + - - +
21B LYS 3.7 1.8 - - - +
23B THR* 1.3 76.0 - - - +
25B LEU* 1.3 66.2 + - - +
27B LYS* 3.0 3.9 + - - +
28B LEU* 2.8 46.3 + - + +
93B ILE* 4.3 15.5 - - + -
95B VAL* 4.2 26.5 - - + -
122B ALA* 5.0 1.3 - - + -
124B ASN* 5.9 0.2 - - - +
154B ILE* 4.2 17.7 - - + -
156B ALA* 3.8 12.7 - - + +
162B VAL* 3.6 29.8 - - + -
165B ILE* 4.9 7.6 - - + -
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Residues in contact with LEU 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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13B ILE* 4.2 13.9 - - + +
21B LYS 2.8 17.7 + - - +
22B SER* 3.4 11.9 - - - +
24B LEU* 1.3 79.0 - - - +
26B ASN* 1.3 60.7 + - - +
28B LEU* 3.3 3.3 + - + +
29B LEU* 3.0 45.6 + - + +
48B VAL* 3.2 49.6 - - + +
49B GLY* 4.8 0.4 - - - -
60B TYR* 4.0 32.3 - - + -
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Residues in contact with ASN 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 SER* 3.0 20.9 + - - +
23B THR* 3.7 7.7 - - - +
24B LEU 3.1 0.4 - - - -
25B LEU* 1.3 78.8 - - - +
27B LYS* 1.3 64.2 + - + +
29B LEU* 3.3 19.0 + - - +
30B GLY* 3.3 17.8 + - - -
31B GLN 4.5 2.1 + - - +
34B SER* 3.5 36.2 + - - +
35B ILE 3.3 26.8 + - - +
36B THR* 3.7 16.2 - - - +
215B THR* 5.1 1.2 - - + +
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Residues in contact with LYS 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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23B THR* 3.2 11.4 + - + +
24B LEU* 3.0 9.3 + - - +
26B ASN* 1.3 77.6 - - + +
28B LEU* 1.3 62.9 + - - +
30B GLY* 3.4 12.7 + - - -
156B ALA 3.1 29.4 - - - +
157B GLU 3.7 14.2 + - - -
158B THR 4.1 3.6 - - - -
159B GLY* 3.9 21.8 - - - +
162B VAL* 3.9 21.4 - - + +
213B SER* 3.3 26.1 + - - +
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Residues in contact with LEU 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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13B ILE* 4.3 9.2 - - + -
24B LEU* 2.8 42.3 + - + +
25B LEU* 3.6 6.3 - - - +
27B LYS* 1.3 79.1 - - - +
29B LEU* 1.3 61.1 + - - +
30B GLY* 3.3 1.2 + - - -
51B HIS* 3.6 21.5 + - - -
60B TYR* 3.9 39.5 - - + +
93B ILE* 4.6 1.1 - - + -
162B VAL* 3.9 21.5 - - + +
165B ILE* 4.4 13.0 - - + -
166B ALA* 4.0 31.4 - - + +
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Residues in contact with LEU 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 LEU* 3.0 46.5 + - + +
26B ASN* 3.3 19.0 + - - +
28B LEU* 1.3 76.5 - - - +
30B GLY* 1.3 62.4 - - - +
31B GLN* 3.2 16.1 + - + +
48B VAL 5.0 0.9 - - - +
49B GLY* 4.2 8.1 - - - -
50B ILE 3.7 41.5 - - - +
51B HIS* 3.5 24.8 + - + +
60B TYR* 4.6 1.8 - - + -
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Residues in contact with GLY 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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26B ASN 3.3 8.5 + - - -
27B LYS* 3.4 10.7 + - - -
28B LEU 3.1 4.2 - - - -
29B LEU* 1.3 77.7 - - - +
31B GLN* 1.3 66.2 + - - +
32B LYS* 3.6 1.9 + - - -
51B HIS* 5.6 0.9 - - - -
212B TYR* 6.2 0.5 - - - -
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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