Contacts of the helix formed by residues 1104 - 1111 (chain A) in PDB entry 1SIW
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 ASN1104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A SER* 2.9 38.7 + - - -
100A TRP* 3.7 26.0 - - - +
101A TYR* 3.7 15.9 - - - +
1101A TYR* 2.8 26.7 + - - +
1103A ASP* 1.3 78.5 + - - +
1105A LEU* 1.3 63.3 + - - +
1106A LEU* 2.9 40.4 + - - +
1107A MET* 3.1 6.5 + - + +
1108A LEU* 2.9 22.5 + - - +
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Residues in contact with LEU1105 (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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100A TRP* 3.7 32.9 - - + +
1103A ASP 3.3 5.3 + - - -
1104A ASN* 1.3 72.4 + - - +
1106A LEU* 1.3 58.3 + - + +
1108A LEU* 4.2 2.7 - - - -
1109A THR* 2.8 45.4 + - - +
104B PHE* 3.6 23.6 - - + +
105B ASP* 3.8 29.8 - - - +
106B PHE* 3.9 29.2 - - + -
108B TYR* 3.8 4.9 + - - +
129B LEU* 5.2 5.4 - - + -
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Residues in contact with LEU1106 (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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97A SER* 3.5 34.1 - - - +
100A TRP* 4.3 17.2 - - + -
1104A ASN* 2.9 10.5 + - - +
1105A LEU* 1.3 76.8 - - - +
1107A MET* 1.3 69.3 + - + +
1109A THR* 3.2 6.2 + - - -
1110A LEU* 3.1 27.2 + - - +
24B VAL* 4.3 9.2 - - + -
27B LYS* 3.6 32.5 - - + -
28B ASN* 3.4 23.3 - - - +
40B TRP* 4.2 13.5 - - + -
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Residues in contact with MET1107 (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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93A PRO* 3.5 25.1 - - + +
94A ARG* 4.0 19.3 - - - -
97A SER* 3.7 19.3 - - - +
1095A TRP* 3.4 55.3 - - + +
1101A TYR* 3.6 22.2 - - + +
1104A ASN* 3.1 9.6 + - + +
1106A LEU* 1.3 79.7 - - - +
1108A LEU* 1.3 62.9 + - - +
1110A LEU* 3.3 10.4 + - + +
1111A GLY* 3.0 20.3 + - - -
24B VAL* 4.0 20.0 - - + -
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Residues in contact with LEU1108 (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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1101A TYR 5.1 0.2 - - - +
1102A SER* 3.5 25.1 - - - +
1103A ASP* 3.8 10.8 - - - +
1104A ASN 2.9 14.5 + - - +
1105A LEU* 3.7 4.0 - - - +
1107A MET* 1.3 77.3 - - - +
1109A THR* 1.3 61.3 + - - +
1111A GLY* 3.4 4.8 + - - -
1113A GLY* 2.9 31.4 + - - +
1114A GLY* 3.5 32.5 - - - +
1115A PRO* 5.7 0.2 - - + -
1169A VAL* 4.1 10.5 - - + -
104B PHE* 4.1 1.1 - - - -
106B PHE* 3.3 38.1 - - + -
108B TYR* 3.8 13.2 - - - +
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Residues in contact with THR1109 (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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1105A LEU* 2.8 38.4 + - - +
1106A LEU* 3.6 6.7 - - - -
1108A LEU* 1.3 77.5 - - - +
1110A LEU* 1.3 60.6 + - - +
1111A GLY 3.5 5.2 + - - +
40B TRP* 3.8 18.8 - - + -
101B TYR* 3.6 30.3 - - + +
104B PHE* 3.9 17.8 + - + -
141B GLY* 4.5 2.8 - - - -
142B PRO* 3.3 24.1 - - + +
143B ASN 4.8 0.3 + - - -
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Residues in contact with LEU1110 (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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1095A TRP* 3.6 22.2 - - + -
1106A LEU* 3.1 18.2 + - + +
1107A MET* 4.0 9.0 - - + +
1109A THR* 1.3 75.0 - - - +
1111A GLY* 1.3 62.6 + - - +
20B HIS* 4.4 24.7 - - + +
23B SER* 5.0 2.0 - - - -
24B VAL* 3.7 30.5 - - + -
40B TRP* 3.4 41.7 - - + -
142B PRO* 4.1 12.1 - - + -
143B ASN* 3.1 38.1 + - + +
146B ASP* 5.0 0.5 - - - +
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Residues in contact with GLY1111 (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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1095A TRP* 3.6 27.6 - - - -
1107A MET 3.0 12.7 + - - -
1108A LEU* 3.4 1.5 + - - -
1109A THR 3.2 6.2 - - - +
1110A LEU* 1.3 83.4 - - - +
1112A ARG* 1.3 65.0 + - - +
1113A GLY 3.6 3.1 + - - -
141B GLY* 5.3 0.5 - - - -
143B ASN 4.5 8.0 - - - +
144B TRP* 4.3 10.2 + - - -
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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