Contacts of the helix formed by residues 23 - 31 (chain A) in PDB entry 1Y1V
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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU 3.3 5.6 + - - -
22A PHE* 1.3 74.3 - - - +
24A PRO* 1.3 72.4 - - - +
25A GLU* 3.2 16.6 + - - +
26A GLU* 2.8 35.0 + - - +
27A VAL* 3.1 8.2 + - - +
233A TRP* 3.3 35.7 - - - +
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Residues in contact with PRO 24 (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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22A PHE 3.4 3.9 - - - +
23A SER* 1.3 80.4 - - - +
25A GLU* 1.3 85.8 + - - +
27A VAL* 3.0 18.3 + - + +
28A ARG* 3.0 24.7 + - - +
233A TRP* 3.4 20.0 - - + +
235A ILE 5.7 2.9 - - - +
237A THR* 4.0 33.9 - - + +
238A CYS* 4.0 18.7 - - + +
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Residues in contact with GLU 25 (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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23A SER* 3.2 15.4 - - - +
24A PRO* 1.3 100.6 - - - +
26A GLU* 1.3 57.5 + - - +
28A ARG* 3.8 10.1 + - - +
29A ALA* 3.1 24.3 + - - +
233A TRP* 4.1 3.9 + - - -
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Residues in contact with GLU 26 (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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22A PHE* 3.0 34.6 - - + -
23A SER* 2.8 25.8 + - - +
25A GLU* 1.3 71.1 - - - +
27A VAL* 1.3 68.6 + - - +
28A ARG 3.1 1.6 - - - -
29A ALA* 2.8 10.2 + - + +
30A ILE* 2.7 35.2 + - + +
1166B CYS* 3.8 14.7 - - - +
1168B LEU* 4.0 2.8 - - - +
1185B CYS* 4.9 4.0 - - - -
1213B THR* 4.3 0.2 - - - +
1215B ARG* 3.3 36.1 + - - -
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Residues in contact with VAL 27 (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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22A PHE* 3.6 38.8 - - + +
23A SER 3.1 5.8 + - - +
24A PRO* 3.0 12.3 + - + +
26A GLU* 1.3 78.6 - - - +
28A ARG* 1.3 61.4 + - - +
30A ILE* 3.7 5.6 + - - +
31A SER* 3.1 20.4 + - - -
81A PHE* 5.9 0.2 - - - +
83A HIS* 3.9 7.0 - - + -
238A CYS* 3.4 42.6 - - - +
240A PRO* 3.8 27.8 - - + -
1211B ASN* 4.9 0.9 - - - +
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Residues in contact with ARG 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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24A PRO* 3.0 22.5 + - - +
25A GLU* 3.9 9.2 - - - +
27A VAL* 1.3 73.0 - - - +
29A ALA* 1.3 69.1 + - - +
31A SER* 2.9 21.6 + - - +
83A HIS* 3.7 29.6 - - + +
85A ASP* 3.4 24.5 + - - +
237A THR* 4.9 15.2 - - - +
238A CYS* 3.8 9.5 - - - +
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Residues in contact with ALA 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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25A GLU 3.1 14.9 + - - +
26A GLU* 2.8 15.5 + - + +
28A ARG* 1.3 80.6 - - - +
30A ILE* 1.3 63.8 + - + +
31A SER 3.3 5.4 + - - +
1183B LYS* 4.4 12.6 - - - +
1184B GLY* 3.8 27.5 - - - +
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Residues in contact with ILE 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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22A PHE* 3.9 24.2 - - + -
26A GLU* 2.7 25.3 + - + +
27A VAL* 4.0 5.2 - - - +
29A ALA* 1.3 74.9 - - + +
31A SER* 1.3 64.9 + - - +
32A VAL* 3.7 11.6 + - - +
80A HIS* 5.9 0.2 - - - +
81A PHE* 3.7 31.8 + - + +
1168B LEU* 3.8 29.2 - - + -
1170B THR* 3.5 31.4 - - + +
1183B LYS* 4.4 12.7 + - - +
1184B GLY* 5.8 0.2 - - - -
1185B CYS* 5.3 7.2 - - - -
1208B MET* 4.2 7.6 - - + -
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Residues in contact with SER 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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27A VAL 3.1 14.7 + - - -
28A ARG 2.9 19.5 + - - +
29A ALA 3.6 3.8 - - - +
30A ILE* 1.3 79.8 - - - +
32A VAL* 1.3 64.0 + - - +
33A ALA 3.2 2.8 + - - -
81A PHE* 2.8 10.1 - - - -
82A GLY* 3.1 3.4 - - - -
83A HIS* 2.8 51.8 + - - -
1183B LYS* 6.2 0.2 - - - +
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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