Contacts of the helix formed by residues 22 - 38 (chain B) in PDB entry 6ICV
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 PRO 22 (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* 1.3 85.1 - - - +
23B LYS* 1.3 62.6 + - + +
24B GLU 3.3 0.2 + - - -
25B ILE* 3.4 8.6 + - + +
26B LEU* 3.1 22.5 + - - +
221B TYR* 4.8 8.6 + - - +
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Residues in contact with LYS 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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21B SER* 3.3 7.7 + - - +
22B PRO* 1.3 79.6 - - - +
24B GLU* 1.3 61.7 + - - +
26B LEU* 3.4 7.7 + - - +
27B ASN* 3.0 23.2 + - - +
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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
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21B SER* 3.2 30.5 + - - +
22B PRO 3.2 0.6 - - - -
23B LYS* 1.3 77.7 - - - +
25B ILE* 1.3 63.1 + - + +
27B ASN* 3.3 6.8 + - + +
28B LEU* 3.0 35.7 + - + +
63B LYS* 3.2 43.5 + - - +
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Residues in contact with ILE 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 SER 3.3 21.0 + - - +
22B PRO* 4.0 6.7 - - + +
24B GLU* 1.3 76.0 - - + +
26B LEU* 1.3 60.9 + - - +
28B LEU* 3.0 14.6 + - + +
29B THR* 2.8 38.6 + - + +
60B ILE* 5.3 5.6 - - + -
63B LYS* 4.5 17.7 - - + +
64B GLN* 4.0 36.8 - - + +
221B TYR* 3.5 35.0 - - + +
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Residues in contact with LEU 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 PRO 3.1 16.9 + - - +
23B LYS* 3.7 8.5 - - - +
25B ILE* 1.3 78.4 - - - +
27B ASN* 1.3 62.4 + - - +
29B THR* 3.0 18.2 + - - -
30B SER* 3.0 19.0 + - - -
221B TYR* 4.5 10.7 - - + -
222B LYS* 5.4 1.9 - - + +
225B GLN* 6.3 1.1 - - + -
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Residues in contact with ASN 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 LYS 3.0 14.2 + - - +
24B GLU* 3.6 10.8 - - + +
25B ILE 3.3 0.2 - - - -
26B LEU* 1.3 75.5 - - - +
28B LEU* 1.3 58.5 + - + +
30B SER* 3.4 7.1 + - - -
31B GLU* 3.0 26.2 + - - +
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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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24B GLU* 3.0 31.9 + - + +
25B ILE* 3.0 12.7 + - + +
27B ASN* 1.3 75.2 - - + +
29B THR* 1.3 60.7 + - - +
31B GLU* 3.2 22.8 + - - +
32B LEU* 2.8 26.9 + - - +
56B LEU* 5.7 4.2 - - + +
59B LYS* 4.3 21.8 - - + -
60B ILE* 3.8 32.0 - - + +
63B LYS* 3.9 29.2 - - + -
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Residues in contact with THR 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 ILE* 2.8 31.5 + - + +
26B LEU* 3.0 17.3 + - - -
28B LEU* 1.3 69.6 - - - +
30B SER* 1.3 55.3 + - - +
32B LEU* 3.1 6.9 + - - -
33B LEU* 2.7 32.6 + - - +
60B ILE* 4.5 8.1 - - + -
217B TYR* 4.0 27.1 - - + -
218B ALA* 3.3 23.8 - - + +
221B TYR* 3.8 25.4 - - + -
222B LYS* 4.4 5.5 - - - +
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Residues in contact with SER 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 LEU* 3.0 21.1 + - - +
27B ASN* 3.5 8.3 - - - -
29B THR* 1.3 77.6 + - - +
31B GLU* 1.3 62.7 + - - +
33B LEU* 3.4 7.1 + - - +
34B GLN* 3.1 23.2 + - - +
222B LYS* 4.7 12.8 - - - +
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Residues in contact with GLU 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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27B ASN 3.0 13.6 + - - +
28B LEU* 3.4 27.4 - - - +
30B SER* 1.3 76.0 - - - +
32B LEU* 1.3 57.3 + - - +
34B GLN* 3.4 8.6 + - + +
35B LYS* 2.9 28.1 + - + +
56B LEU* 3.7 31.3 - - + +
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Residues in contact with LEU 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 LEU 2.8 14.2 + - - +
29B THR* 3.1 8.7 + - - +
31B GLU* 1.3 77.9 - - - +
33B LEU* 1.3 57.4 + - - +
35B LYS* 3.1 0.9 + - - +
36B CYS* 2.9 55.7 + - - -
53B ILE* 4.3 3.4 - - + -
56B LEU* 3.9 32.3 - - + +
57B VAL* 4.0 15.5 - - + -
60B ILE* 3.8 22.4 - - + -
214B ALA* 3.9 34.1 - - + +
217B TYR* 4.5 12.6 - - + -
218B ALA* 4.0 6.7 - - + -
241B TYR* 5.5 0.9 - - + -
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Residues in contact with LEU 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 THR 2.7 20.2 + - - +
30B SER* 3.8 7.2 - - - +
31B GLU 3.4 0.2 - - - -
32B LEU* 1.3 72.0 - - - +
34B GLN* 1.3 62.4 + - - +
36B CYS* 3.4 2.5 + - - -
37B SER* 2.7 44.2 + - - +
215B ARG* 3.8 28.5 - - + +
218B ALA* 3.5 11.8 - - + +
219B TYR* 4.0 30.1 - - + -
222B LYS* 5.3 9.2 - - + -
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Residues in contact with GLN 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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30B SER 3.1 16.7 + - - +
31B GLU* 3.7 7.2 - - + +
33B LEU* 1.3 76.6 - - - +
35B LYS* 1.3 65.0 + - + +
37B SER* 3.3 13.5 + - - -
38B SER* 3.3 13.5 + - - -
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Residues in contact with LYS 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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31B GLU* 2.9 19.0 + - + +
32B LEU* 3.1 4.9 + - - +
34B GLN* 1.3 81.7 - - + +
36B CYS* 1.3 60.5 + - - +
37B SER 3.6 0.3 + - - -
38B SER* 3.6 16.2 + - - -
49B GLU* 4.6 14.0 - - - +
52B GLN* 2.7 41.4 + - - -
53B ILE* 3.9 24.1 - - + +
56B LEU* 3.9 21.5 - - + -
211B LYS* 4.3 5.2 - - - -
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Residues in contact with CYS 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 LEU* 2.9 26.0 + - - +
33B LEU 3.7 1.1 - - - -
35B LYS* 1.3 75.7 - - - +
37B SER* 1.3 59.2 + - - +
38B SER 3.5 0.6 - - - +
53B ILE* 3.6 38.8 - - - -
211B LYS* 3.5 22.5 - - + +
214B ALA* 3.7 17.0 - - - -
215B ARG* 3.0 47.7 + - + -
82D MET* 4.6 0.2 - - - +
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Residues in contact with SER 37 (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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33B LEU* 2.7 38.5 + - - +
34B GLN* 3.3 6.9 + - - -
36B CYS* 1.3 77.5 - - - +
38B SER* 1.3 65.9 + - - +
39B PRO* 3.7 2.4 - - - +
215B ARG* 3.8 11.0 - - - +
82D MET* 4.1 21.6 - - - +
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Residues in contact with SER 38 (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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34B GLN 3.3 10.6 + - - -
35B LYS* 3.7 17.3 - - - -
36B CYS 3.5 1.4 - - - +
37B SER* 1.3 82.1 - - - +
39B PRO* 1.3 74.1 - - - +
49B GLU* 5.3 2.0 - - - -
211B LYS* 2.9 23.6 + - - -
82D MET* 5.5 1.7 - - - +
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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