Contacts of the helix formed by residues 23 - 36 (chain B) in PDB entry 6I4X
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 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B SER 4.8 4.5 - - - +
22B SER* 1.3 81.8 + - - +
24B VAL* 1.3 65.3 + - - +
25B PHE* 3.7 5.4 + - - +
26B GLU* 3.3 31.0 + - + +
27B LEU* 3.2 18.7 + - - +
53B ASP 3.6 12.6 + - - -
54B GLY* 3.8 16.2 - - - +
55B LYS 3.5 6.1 - - - +
56B THR* 4.1 3.8 - - - +
57B LEU* 4.1 3.6 - - - +
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Residues in contact with VAL 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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23B THR* 1.3 74.0 - - - +
25B PHE* 1.3 63.9 + - - +
27B LEU* 3.0 6.1 + - - +
28B LYS* 3.0 31.6 + - - +
44B LEU* 3.9 19.7 - - + -
51B LEU* 3.9 20.0 - - + +
52B ASP 3.3 28.5 - - - +
53B ASP* 3.5 7.2 + - - +
55B LYS 3.1 7.5 + - - +
57B LEU* 3.9 17.5 - - + -
60B CYS* 3.6 28.0 - - - -
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 3.2 4.5 - - - +
24B VAL* 1.3 77.4 - - - +
26B GLU* 1.3 79.0 + - + +
28B LYS* 3.1 9.0 + - - +
29B ARG* 3.0 43.8 + - + +
39B PRO* 3.8 26.7 - - + -
53B ASP* 3.1 44.9 + - + +
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Residues in contact with GLU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 4.9 8.3 - - - -
23B THR* 3.3 27.1 + - + +
25B PHE* 1.3 97.8 - - + +
27B LEU* 1.3 59.8 + - - +
29B ARG* 3.3 16.8 + - - +
30B ILE* 3.2 25.9 + - - +
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Residues in contact with LEU 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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5B LEU* 3.8 32.8 - - + -
7B ILE* 4.1 20.4 - - + -
16B THR* 4.4 10.1 - - + -
18B ALA* 4.9 6.5 - - + -
22B SER* 5.8 0.6 + - - +
23B THR 3.2 10.4 + - - +
24B VAL* 3.0 12.8 + - + +
26B GLU* 1.3 74.8 - - - +
28B LYS* 1.3 64.0 + - - +
30B ILE* 3.0 33.2 + - + +
31B VAL* 3.1 18.5 + - + +
44B LEU* 3.7 22.2 - - + -
51B LEU* 6.0 1.8 - - + -
57B LEU* 4.2 18.4 - - + -
62B PHE* 6.1 0.9 - - + -
75B VAL* 4.8 7.2 - - + -
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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
----------------------------------------------------------
24B VAL* 3.0 23.0 + - - +
25B PHE* 3.1 8.5 + - - +
27B LEU* 1.3 75.2 - - - +
29B ARG* 1.3 57.4 + - - +
31B VAL* 3.2 2.7 + - - -
32B GLU* 2.9 23.4 + - - +
39B PRO* 3.7 33.2 + - + +
42B GLN* 3.0 56.1 + - + +
43B ARG* 4.2 4.2 - - - +
44B LEU* 3.7 31.1 - - + +
51B LEU 4.7 5.0 + - - -
53B ASP* 3.0 33.7 + - - +
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Residues in contact with ARG 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 PHE* 3.0 40.5 + - + +
26B GLU* 3.4 23.1 - - - +
27B LEU 3.2 0.4 - - - -
28B LYS* 1.3 74.6 - - - +
30B ILE* 1.3 64.1 + - - +
32B GLU* 3.3 33.4 + - - +
33B GLY* 3.3 10.7 + - - -
39B PRO* 4.1 11.4 - - + -
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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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14B ILE* 5.8 0.7 - - + -
16B THR* 3.8 26.5 - - + +
17B ASP 4.2 17.9 - - - +
18B ALA* 4.6 7.9 - - + -
26B GLU 3.2 15.6 + - - +
27B LEU* 3.0 25.2 + - + +
29B ARG* 1.3 74.4 - - + +
31B VAL* 1.3 66.3 + - + +
32B GLU 3.3 0.2 + - - -
33B GLY* 3.4 9.9 + - - -
34B ILE* 3.6 20.2 - - + +
18C TYR* 4.3 10.5 - - + +
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Residues in contact with VAL 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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7B ILE* 4.2 25.4 - - + -
14B ILE* 4.5 9.6 - - + -
27B LEU* 3.1 17.9 + - + +
28B LYS* 3.2 1.8 + - - +
30B ILE* 1.3 78.8 - - + +
32B GLU* 1.3 57.3 + - - +
34B ILE* 3.2 4.1 + - - +
35B LEU* 2.9 45.0 + - + +
37B ARG* 4.7 0.6 + - + -
42B GLN* 3.4 28.0 - - - +
44B LEU* 4.9 6.5 - - + -
77B LEU* 3.9 25.8 - - + -
79B PHE* 4.9 2.2 - - + -
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Residues in contact with GLU 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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28B LYS 2.9 12.7 + - - +
29B ARG* 3.4 34.0 - - - +
30B ILE 3.2 0.4 - - - -
31B VAL* 1.3 77.8 - - - +
33B GLY* 1.3 58.1 + - - +
34B ILE 3.1 0.2 - - - -
36B LYS* 3.0 32.1 + - - +
37B ARG 3.2 29.2 - - - +
38B PRO* 3.4 24.9 - - + +
39B PRO* 3.8 4.2 - - + +
42B GLN* 3.8 0.4 - - - +
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Residues in contact with GLY 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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29B ARG 3.3 9.5 + - - -
30B ILE 3.4 3.7 + - - -
31B VAL 3.3 0.4 - - - -
32B GLU* 1.3 78.4 - - - +
34B ILE* 1.3 62.5 + - - +
36B LYS* 4.7 11.4 - - - -
17C MET* 5.7 4.7 - - - +
18C TYR* 5.9 0.5 - - - -
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Residues in contact with ILE 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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14B ILE* 3.8 32.5 - - + -
30B ILE* 3.6 19.7 - - + +
31B VAL 3.2 5.5 + - - +
32B GLU 3.1 0.6 - - - -
33B GLY* 1.3 82.1 - - - +
35B LEU* 1.3 79.0 + - + +
36B LYS* 3.4 9.8 + - - +
18C TYR* 3.5 52.5 - - + +
30C ILE* 3.8 20.9 - - + -
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Residues in contact with LEU 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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9B ARG* 5.3 3.4 - - + -
12B THR* 4.6 13.0 - - + -
14B ILE* 3.9 18.8 - - + -
31B VAL* 2.9 17.2 + - + +
34B ILE* 1.3 89.0 - - + +
36B LYS* 1.3 73.7 + - - +
37B ARG* 3.3 9.5 + - + +
77B LEU* 4.0 15.9 - - + -
79B PHE* 3.7 34.8 - - + -
30C ILE* 3.8 18.8 - - + -
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Residues in contact with LYS 36 (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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32B GLU* 3.0 19.0 + - - +
33B GLY* 4.7 11.7 - - - +
34B ILE 4.3 8.3 - - - +
35B LEU* 1.3 80.4 - - - +
37B ARG* 1.3 68.5 + - - +
38B PRO* 4.3 4.1 - - - +
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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