Contacts of the helix formed by residues 1027 - 1037 (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 ASP1027 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025A GLY 3.2 0.2 - - - -
1026A ASP* 1.3 80.8 - - - +
1028A PRO* 1.4 62.5 - - - +
1029A LEU 3.3 0.7 + - - -
1030A SER* 3.0 18.2 + - - +
1031A ARG* 2.4 39.2 + - - +
162E ARG* 2.3 63.3 + - + +
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Residues in contact with PRO1028 (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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1026A ASP 4.3 2.7 - - - +
1027A ASP* 1.4 94.8 - - - +
1029A LEU* 1.3 54.2 + - - +
1031A ARG* 3.5 31.0 - - - +
1032A GLN* 3.0 27.5 + - - +
162E ARG* 3.7 11.0 - - - +
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Residues in contact with LEU1029 (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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1028A PRO* 1.3 75.0 - - - +
1030A SER* 1.3 59.2 + - - +
1032A GLN* 3.3 18.7 + - - +
1033A ALA* 2.8 28.7 + - + +
151E MET* 6.4 2.7 - - + -
155E GLU 5.8 0.4 - - - +
158E GLU* 5.9 0.7 - - + -
159E LEU* 3.7 36.6 - - + -
162E ARG* 2.9 46.7 - - + +
163E TYR* 4.5 10.3 - - + +
206E TYR* 3.9 17.5 - - + +
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Residues in contact with SER1030 (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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890A ARG* 4.4 6.2 + - - +
1024A ASN 3.8 8.4 + - - -
1025A GLY* 3.6 22.4 - - - -
1027A ASP* 3.0 23.4 + - - +
1029A LEU* 1.3 75.9 - - - +
1031A ARG* 1.3 59.2 + - - +
1033A ALA* 3.3 8.3 + - - +
1034A GLN* 2.9 28.4 + - - +
162E ARG* 4.8 12.0 + - - +
163E TYR* 6.0 3.8 - - - -
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Residues in contact with ARG1031 (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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1025A GLY* 4.2 13.6 + - - +
1026A ASP* 3.4 32.9 + - - +
1027A ASP 2.4 20.5 + - - +
1028A PRO* 3.5 33.1 - - - +
1030A SER* 1.3 73.2 - - - +
1032A GLN* 1.3 58.0 + - - +
1034A GLN* 3.3 8.8 + - + +
1035A GLU* 3.1 27.0 + - - +
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Residues in contact with GLN1032 (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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1028A PRO 3.0 18.6 + - - +
1029A LEU* 3.5 16.6 - - - +
1031A ARG* 1.3 74.8 - - - +
1033A ALA* 1.3 62.2 + - - +
1035A GLU* 3.2 23.8 + - + +
1036A ASN* 2.9 21.9 + - + +
192E LYS* 5.6 7.3 - - - +
204E ILE* 3.4 28.5 - - + +
206E TYR* 5.9 0.4 + - - -
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Residues in contact with ALA1033 (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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890A ARG* 3.6 19.1 + - - +
1029A LEU* 2.8 19.9 + - + +
1030A SER* 3.3 8.9 + - - +
1032A GLN* 1.3 73.4 - - - +
1034A GLN* 1.3 59.2 + - - +
1036A ASN* 3.5 11.1 + - - +
1037A ALA* 3.1 30.1 + - - +
163E TYR* 4.2 17.5 - - - +
204E ILE* 5.7 2.5 - - + -
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Residues in contact with GLN1034 (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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890A ARG* 2.9 26.9 + - - +
1017A SER 5.8 0.6 + - - -
1020A LEU 3.8 5.1 + - - -
1021A VAL* 3.0 24.0 - - + +
1022A ILE* 2.9 29.6 - - - +
1023A VAL 3.1 22.6 + - - +
1025A GLY* 5.6 2.9 - - - +
1030A SER 2.9 13.4 + - - +
1031A ARG* 3.4 12.3 - - - +
1033A ALA* 1.3 79.0 - - - +
1035A GLU* 1.3 62.4 + - - +
1036A ASN 3.6 0.2 + - - -
1037A ALA* 3.7 0.5 + - - +
1038A THR* 3.4 29.3 + - - +
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Residues in contact with GLU1035 (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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1031A ARG* 3.1 11.6 + - - +
1032A GLN* 3.2 19.8 + - + +
1034A GLN* 1.3 79.6 - - - +
1036A ASN* 1.3 61.4 + - + +
1038A THR* 4.1 3.6 + - - -
1039A LEU* 3.3 24.7 + - + +
1042A ASN* 5.8 0.3 - - - +
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Residues in contact with ASN1036 (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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1032A GLN* 2.9 20.5 + - + +
1033A ALA* 3.5 12.3 + - - +
1035A GLU* 1.3 75.8 - - + +
1037A ALA* 1.3 81.6 - - - +
1038A THR 3.1 9.8 + - - -
1039A LEU* 3.3 21.4 + - - +
200E ALA 3.6 5.9 - - - +
202E ARG* 3.2 55.0 + - + +
203E TYR* 4.6 5.3 - - - +
204E ILE* 3.4 30.1 - - + +
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Residues in contact with ALA1037 (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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890A ARG* 3.9 20.0 - - - +
893A GLU 5.3 1.1 - - - +
894A ASP* 4.3 17.8 - - - +
1022A ILE* 4.1 9.2 - - + -
1033A ALA 3.1 18.5 + - - +
1034A GLN 4.2 2.7 - - - +
1035A GLU 3.5 0.6 - - - -
1036A ASN* 1.3 86.4 - - - +
1038A THR* 1.3 65.0 + - - +
1039A LEU 3.7 0.2 - - - -
200E ALA* 3.8 22.1 - - + +
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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