Contacts of the helix formed by residues 27 - 35 (chain A) 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 SER 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL 4.0 1.0 + - - -
26A LEU* 1.3 73.5 - - - +
28A PRO* 1.3 58.5 - - - +
29A ASP* 3.2 19.8 + - - +
30A GLU* 3.0 23.0 + - - +
31A LEU* 2.4 37.2 + - - +
33A ARG* 5.2 1.6 + - - -
247A TRP* 3.9 34.1 + - - -
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Residues in contact with PRO 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.7 6.0 - - + +
27A SER* 1.3 88.6 - - - +
29A ASP* 1.3 54.7 + - + +
31A LEU* 3.5 12.5 - - + +
32A LYS* 2.8 39.6 + - - +
222A HIS* 6.2 2.2 - - + +
247A TRP* 3.7 31.6 - - + +
249A ILE 5.9 1.3 - - - +
251A THR* 3.3 27.6 - - + +
252A VAL* 3.9 17.5 - - + +
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 3.2 10.0 + - - +
28A PRO* 1.3 83.3 - - + +
30A GLU* 1.3 60.7 + - - +
32A LYS* 3.6 23.1 + - - +
33A ARG* 3.4 42.5 + - - +
230R GLU* 5.6 2.4 - - - +
233R ILE* 5.6 5.9 - - - +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 5.9 2.0 - - + -
27A SER* 3.0 25.9 + - - +
29A ASP* 1.3 77.8 - - - +
31A LEU* 1.3 59.0 + - - +
32A LYS 3.2 0.2 - - - -
33A ARG* 2.5 50.8 + - - +
34A MET* 2.9 49.0 + - + +
1122B CYS* 5.6 3.5 - - - -
1124B ILE* 5.8 2.8 - - + +
1138B ARG 5.3 0.2 - - - +
1139B GLY* 4.1 21.1 - - - +
1140B CYS* 4.6 7.5 + - - -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.1 28.0 - - + -
27A SER 2.4 30.0 + - - +
28A PRO* 3.2 9.4 + - + +
30A GLU* 1.3 68.5 - - - +
32A LYS* 1.3 62.2 + - - +
34A MET* 3.2 31.9 + - + +
35A SER* 3.5 6.8 + - - +
85A PHE* 5.7 6.7 - - + -
86A GLY 5.0 3.4 - - - +
87A HIS* 4.4 10.3 - - + -
252A VAL* 3.7 40.4 - - + +
253A LEU 4.2 0.2 - - - -
254A PRO* 3.8 35.4 - - + -
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO 2.8 21.4 + - - +
29A ASP* 3.7 24.9 + - - +
31A LEU* 1.3 74.5 - - - +
33A ARG* 1.3 63.3 + - - +
34A MET 3.4 0.2 + - - -
35A SER 3.9 12.8 + - - +
38A GLU* 6.1 1.0 - - - +
87A HIS* 4.3 23.0 + - + +
89A GLU* 5.2 14.1 + - + +
252A VAL* 4.1 25.1 - - + +
227R SER* 5.5 8.3 + - - -
230R GLU* 4.9 10.3 + - - -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 5.2 1.2 + - - -
29A ASP* 3.4 30.7 + - - +
30A GLU* 2.5 58.9 + - - +
32A LYS* 1.3 78.8 - - + +
34A MET* 1.3 63.0 + - - +
35A SER 4.5 0.3 - - - +
1138B ARG* 3.8 18.2 + - - +
1139B GLY* 3.8 33.2 + - - -
1141B ARG* 5.2 8.5 - - - +
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Residues in contact with MET 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 5.7 10.1 - - + -
30A GLU* 2.9 41.9 + - + +
31A LEU* 3.2 22.8 + - + +
33A ARG* 1.3 80.3 - - - +
35A SER* 1.3 66.0 + - - +
36A VAL 3.5 0.3 + - - -
85A PHE* 4.1 23.3 - - + -
1122B CYS* 6.1 1.8 - - - -
1124B ILE* 3.7 39.5 - - + -
1126B ALA* 3.7 22.5 - - + +
1138B ARG* 3.3 24.5 - - - +
1139B GLY* 5.2 2.9 - - - +
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.5 4.7 + - - -
32A LYS 3.9 10.4 + - - +
33A ARG 3.8 0.5 - - - +
34A MET* 1.3 80.2 - - - +
36A VAL* 1.3 63.8 + - - +
37A THR* 3.0 27.7 + - - +
38A GLU* 4.1 10.0 + - - +
85A PHE* 3.0 20.0 + - - -
86A GLY* 3.0 24.2 - - - -
87A HIS* 3.8 15.2 - - - -
1138B ARG* 4.1 4.9 + - - -
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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