Contacts of the helix formed by residues 25 - 37 (chain B) in PDB entry 5IYB
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.6 13.9 - - + -
22B TRP* 2.3 36.5 + - + +
24B GLU* 1.3 67.1 - - - +
26B CYS* 1.3 55.9 + - - +
27B TRP 3.2 1.3 - - - -
28B ILE* 2.9 41.6 + - + +
29B VAL* 4.0 1.2 + - - +
640B ILE* 4.3 23.1 - - + +
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Residues in contact with CYS 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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21B LEU* 5.8 1.5 - - - +
23B GLN* 3.1 41.3 + - + +
25B ALA* 1.3 75.5 - - - +
27B TRP* 1.3 71.3 + - - +
28B ILE 3.0 0.2 - - - -
29B VAL* 2.7 36.7 + - + +
30B ILE* 2.9 22.1 + - + +
640B ILE* 5.7 0.4 - - - -
698B ILE* 3.8 24.5 - - + +
699B HIS* 4.2 15.9 - - - -
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Residues in contact with TRP 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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24B GLU* 3.9 34.1 + - - +
25B ALA 3.1 1.2 + - - -
26B CYS* 1.3 85.8 - - - +
28B ILE* 1.3 54.8 + - + +
30B ILE* 3.5 31.9 - - + -
31B SER* 2.7 40.3 + - - +
699B HIS* 3.6 34.8 + + - -
701B SER* 4.1 14.8 - - - -
702B MET* 4.3 11.9 - - + -
762B ARG* 3.1 54.4 - - + +
763B SER* 4.8 2.5 - - - -
766B TYR* 3.5 25.4 - + - +
1000B THR* 4.2 9.3 + - + +
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Residues in contact with ILE 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 5.6 0.7 - - - +
25B ALA* 2.9 22.6 + - + +
27B TRP* 1.3 79.8 - - + +
29B VAL* 1.3 58.1 + - + +
31B SER* 4.0 4.9 - - - -
32B SER* 2.8 29.0 + - - +
640B ILE* 4.2 14.1 - - + +
643B LEU* 3.9 28.3 - - + +
644B LYS* 3.9 36.8 - - + +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS* 2.7 24.5 + - + +
28B ILE* 1.3 73.3 - - - +
30B ILE* 1.3 64.1 + - + +
32B SER* 3.1 14.9 + - - -
33B TYR 3.2 8.1 + - - -
626B LEU* 5.2 10.3 - - + -
635B LEU* 4.3 15.3 - - + -
640B ILE* 3.8 28.3 - - + -
643B LEU* 4.2 12.1 - - + -
653B TRP* 4.0 13.9 - - + -
656B LEU* 3.9 24.2 - - + -
662B VAL* 5.6 0.7 - - + -
698B ILE* 5.5 8.1 - - + -
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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
----------------------------------------------------------
26B CYS* 2.9 20.9 + - + +
27B TRP* 3.5 41.5 - - + +
29B VAL* 1.3 71.6 - - + +
31B SER* 1.3 64.9 + - - +
33B TYR* 3.0 23.4 + - + +
34B PHE* 3.3 28.5 + - + -
653B TRP* 5.8 0.2 - - - -
698B ILE* 3.9 29.8 - - + +
699B HIS* 3.7 24.9 - - + -
702B MET* 4.4 14.4 - - + -
766B TYR* 4.2 4.9 - - + -
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TRP* 2.7 27.5 + - - +
28B ILE* 4.0 6.2 - - - -
30B ILE* 1.3 73.7 - - - +
32B SER* 1.3 52.7 + - - +
34B PHE* 3.3 1.6 + - - +
35B ASP* 2.6 42.2 + - - +
766B TYR* 3.2 33.6 + - - -
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Residues in contact with SER 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 ILE* 2.8 17.9 + - - +
29B VAL* 3.1 12.2 + - - -
31B SER* 1.3 75.1 - - - +
33B TYR* 1.3 65.0 + - - +
35B ASP* 4.0 7.0 - - - -
36B GLU* 3.1 25.6 + - - +
643B LEU* 3.7 30.2 + - - +
646B ARG* 5.6 7.8 + - - +
652B SER* 5.9 0.4 - - - -
653B TRP* 3.3 19.4 - - - +
656B LEU* 6.2 0.2 - - - -
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Residues in contact with TYR 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 VAL 3.2 5.1 + - - -
30B ILE* 3.0 16.4 + - + +
32B SER* 1.3 79.5 - - - +
34B PHE* 1.3 83.0 + + - +
36B GLU* 3.7 0.3 - - - +
37B LYS* 2.6 66.1 + - + +
38B GLY 4.7 1.8 - - - -
42B GLN* 5.4 0.3 + - - -
528B LEU 4.6 3.6 - - - -
529B MET* 3.4 26.2 + - + -
530B ALA 3.8 3.5 + - - -
531B TYR* 3.5 23.9 - - - -
624B PRO* 3.5 22.1 - - + +
653B TRP* 3.4 43.7 - + + -
664B TYR* 4.1 6.5 - + - -
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Residues in contact with PHE 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 ILE* 3.3 26.1 + - + -
31B SER 4.1 2.7 - - - +
33B TYR* 1.3 95.4 - + - +
35B ASP* 1.3 62.9 + - - +
37B LYS 2.5 23.7 - - - +
38B GLY 4.5 7.9 - - - +
39B LEU* 3.8 27.7 + - + -
483B ARG* 5.0 0.4 - - - -
528B LEU* 3.7 50.9 - - + -
529B MET* 4.7 1.6 - - + -
702B MET* 4.5 6.5 - - - -
766B TYR* 3.5 49.8 - + + +
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Residues in contact with ASP 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 SER* 2.6 28.1 + - - +
32B SER* 4.1 3.6 - - - -
34B PHE* 1.3 74.4 - - - +
36B GLU* 1.3 61.0 + - - +
37B LYS 4.1 0.3 - - - +
646B ARG* 2.4 43.8 + - - +
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Residues in contact with GLU 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 SER 3.1 19.9 + - - +
35B ASP* 1.3 77.5 - - - +
37B LYS* 1.3 90.9 + - + +
38B GLY 3.6 0.7 + - - -
41B ARG* 3.8 12.3 + - - -
646B ARG* 5.5 1.5 - - - +
652B SER* 5.1 7.4 + - - +
653B TRP* 3.7 36.1 - - + +
654B GLN* 4.0 19.8 - - + +
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Residues in contact with LYS 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 TYR* 2.6 54.2 + - + +
34B PHE 2.5 27.5 - - - +
35B ASP 4.1 0.7 - - - +
36B GLU* 1.3 93.5 + - + +
38B GLY* 1.3 70.1 + - - +
41B ARG* 4.0 20.2 - - + +
531B TYR* 3.7 33.7 + - + -
653B TRP* 4.6 1.6 - - - +
654B GLN* 3.7 22.1 + - - +
664B TYR* 3.9 18.4 - - - -
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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