Contacts of the helix formed by residues 22 - 35 (chain B) in PDB entry 2IBI
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 THR 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B SER 3.4 2.7 + - - +
21B ASP* 1.3 74.7 - - - +
23B ILE* 1.3 60.7 + - - +
24B GLU* 3.2 20.9 + - - +
25B ASN* 2.9 25.8 + - - +
26B VAL* 2.8 30.7 + - - +
53B GLY* 5.3 5.2 - - - +
54B ARG 3.4 9.2 - - - +
55B THR* 4.0 15.5 - - + -
56B LEU 5.3 0.2 - - - -
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Residues in contact with ILE 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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22B THR* 1.3 71.7 - - - +
24B GLU* 1.3 50.9 + - - +
26B VAL* 3.1 7.1 + - + +
27B LYS* 2.7 46.2 + - - +
43B LEU* 4.2 7.6 - - + -
50B LEU* 3.8 42.8 - - + +
51B GLU 3.4 13.5 - - - +
52B ASP* 3.4 15.7 - - - +
54B ARG 3.0 32.2 + - - +
55B THR 4.0 6.1 - - - +
56B LEU* 4.9 7.0 - - + -
59B TYR* 3.2 35.2 - - + -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 3.2 21.8 - - - +
23B ILE* 1.3 73.2 + - - +
25B ASN* 1.3 63.8 + - - +
27B LYS* 3.1 8.6 + - - +
28B ALA* 3.0 21.5 + - - +
38B PRO* 5.4 2.3 - - - +
52B ASP* 3.3 27.4 + - + +
53B GLY* 2.5 38.7 + - - -
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Residues in contact with ASN 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 ASP* 3.1 27.1 - - + +
22B THR* 2.9 28.0 + - - +
24B GLU* 1.3 75.4 - - - +
26B VAL* 1.3 63.0 + - - +
28B ALA* 3.2 20.5 + - - +
29B LYS* 3.2 30.4 + - - +
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Residues in contact with VAL 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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3B ILE* 4.8 1.1 - - + -
15B LEU* 4.0 13.9 - - + -
17B VAL* 4.6 9.4 - - + -
21B ASP* 4.2 7.6 - - + +
22B THR 2.8 19.3 + - - +
23B ILE* 3.4 9.9 - - + +
25B ASN* 1.3 73.1 - - - +
27B LYS* 1.3 61.9 + - - +
29B LYS* 3.2 11.3 + - - +
30B ILE* 3.1 23.9 + - + +
43B LEU* 4.1 11.7 - - + -
50B LEU* 5.9 0.2 - - + -
56B LEU* 3.7 36.1 - - + -
67B LEU* 3.9 27.1 - - + -
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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
----------------------------------------------------------
23B ILE* 2.7 27.1 + - - +
24B GLU* 3.1 9.6 + - - +
26B VAL* 1.3 72.4 - - - +
28B ALA* 1.3 55.7 + - - +
30B ILE* 3.3 1.3 + - - +
31B GLN* 2.8 26.2 + - - +
38B PRO* 3.6 36.9 + - + +
41B GLN* 3.0 53.4 + - - +
42B ARG* 5.3 1.1 - - - +
43B LEU* 3.9 16.4 - - + +
50B LEU 4.4 9.0 + - - -
52B ASP* 3.0 37.7 + - - +
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Residues in contact with ALA 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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24B GLU 3.0 12.6 + - - +
25B ASN* 3.2 17.7 + - - +
27B LYS* 1.3 73.0 - - - +
29B LYS* 1.3 56.5 + - + +
31B GLN* 3.3 15.4 + - - +
32B ASP* 2.7 44.4 + - - +
38B PRO* 4.6 3.5 - - + +
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Residues in contact with LYS 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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15B LEU* 4.3 18.4 - - + -
16B GLU 3.0 26.6 + - - +
17B VAL* 4.1 9.7 - - + +
21B ASP* 2.9 23.1 + - - +
25B ASN* 3.2 35.7 + - - +
26B VAL* 3.4 10.8 - - - +
28B ALA* 1.3 77.6 - - + +
30B ILE* 1.3 61.1 + - - +
32B ASP* 3.3 13.4 + - - +
33B LYS* 3.2 26.3 + - - +
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Residues in contact with ILE 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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5B VAL* 4.0 23.1 - - + -
13B ILE* 4.4 12.3 - - + -
15B LEU* 3.9 12.3 - - + -
26B VAL* 3.1 19.0 + - + +
27B LYS 3.7 1.3 - - - +
28B ALA 3.3 0.2 - - - -
29B LYS* 1.3 72.6 - - - +
31B GLN* 1.3 60.5 + - - +
33B LYS* 3.1 1.6 + - - -
34B GLU* 2.8 45.5 + - + +
36B ILE* 5.4 1.6 - - + +
41B GLN* 3.4 25.6 - - + +
43B LEU* 3.5 37.5 - - + -
69B LEU* 4.4 15.9 - - + -
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Residues in contact with GLN 31 (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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509A ARG* 4.1 2.6 + - - -
27B LYS 2.8 16.2 + - - +
28B ALA* 3.6 10.5 + - - +
30B ILE* 1.3 75.4 - - - +
32B ASP* 1.3 63.5 + - - +
35B GLY* 2.8 32.0 + - - +
36B ILE 3.3 25.4 - - - +
37B PRO* 3.9 10.7 - - - +
38B PRO* 3.6 27.4 - - + +
41B GLN* 3.6 1.9 - - - +
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Residues in contact with ASP 32 (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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509A ARG* 4.2 7.6 + - - -
28B ALA* 2.7 30.6 + - - +
29B LYS* 3.3 13.8 - - - +
31B GLN* 1.3 76.5 + - - +
33B LYS* 1.3 62.7 + - + +
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Residues in contact with LYS 33 (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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471A ASP* 3.4 43.6 + - - +
472A ALA* 5.5 0.2 - - - +
509A ARG* 2.9 17.2 + - - -
13B ILE* 4.2 20.6 - - + +
14B THR 3.5 24.1 + - - +
15B LEU* 4.1 17.0 - - + +
29B LYS* 3.2 9.3 + - - +
30B ILE 3.1 4.2 + - - +
32B ASP* 1.3 83.0 - - + +
34B GLU* 1.3 71.7 - - - +
35B GLY 3.6 0.4 - - - -
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Residues in contact with GLU 34 (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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507A GLU* 4.5 8.1 - - - +
509A ARG* 3.3 25.2 + - - +
7B THR* 3.5 27.6 + - + +
11B LYS* 4.9 11.8 - - - +
13B ILE* 3.9 36.5 - - + +
30B ILE* 2.8 23.7 + - + +
33B LYS* 1.3 89.4 - - - +
35B GLY* 1.3 64.1 + - - +
36B ILE* 3.4 25.4 + - + +
69B LEU* 5.4 0.2 - - + -
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Residues in contact with GLY 35 (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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508A SER 4.4 0.5 - - - +
509A ARG* 3.4 48.2 - - - +
31B GLN* 2.8 24.1 + - - -
34B GLU* 1.3 78.2 - - - +
36B ILE* 1.3 59.7 + - - +
37B PRO* 3.7 7.0 - - - +
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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