Contacts of the helix formed by residues 119 - 129 (chain A) in PDB entry 1S89
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 ASN 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.6 16.5 - - - -
117A ALA* 3.6 1.1 - - - +
118A THR* 1.3 81.4 + - - +
120A VAL* 1.3 61.4 + - - +
122A THR* 2.6 42.6 + - - -
123A ALA* 3.1 14.2 + - - +
109B ALA 3.3 19.4 + - - -
110B THR* 3.9 19.4 - - + +
113B ASN* 3.3 13.7 - - - +
114B ILE 2.8 28.2 + - - +
116B VAL* 4.0 5.5 - - - +
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Residues in contact with VAL 120 (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 MET* 4.8 23.1 - - + +
29A TRP* 4.1 17.0 - - + -
32A ARG* 4.4 9.9 - - - +
89A PHE* 4.0 25.8 - - + -
119A ASN* 1.3 71.5 - - - +
121A ALA* 1.3 61.8 + - - +
123A ALA* 3.1 2.8 + - - +
124A ASP* 2.8 44.7 + - - +
113B ASN* 3.1 14.4 + - - +
139B LEU* 5.1 12.6 - - + -
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Residues in contact with ALA 121 (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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119A ASN* 4.0 0.4 - - - +
120A VAL* 1.3 73.6 - - - +
122A THR* 1.3 62.1 + - - +
124A ASP* 3.4 5.4 + - - +
125A PHE* 3.1 32.2 + - + -
113B ASN* 2.8 46.7 + - - +
115B PRO* 4.0 17.0 - - + -
138B ILE* 4.0 17.0 - - + -
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Residues in contact with THR 122 (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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116A VAL 3.7 5.2 - - - +
117A ALA* 3.6 26.0 - - + -
118A THR* 4.4 2.3 + - - +
119A ASN* 2.6 28.1 + - - -
121A ALA* 1.3 76.3 - - - +
123A ALA* 1.3 63.2 + - - +
125A PHE* 3.3 5.5 + - - +
126A ILE* 3.0 29.3 + - + +
114B ILE 3.5 0.5 + - - -
115B PRO* 3.3 6.0 - - - +
116B VAL* 3.0 44.0 + - - +
122B THR* 4.4 0.2 - - + -
126B ILE* 4.4 9.2 - - + -
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Residues in contact with ALA 123 (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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29A TRP* 3.5 31.5 - - + +
87A ILE* 4.5 6.7 - - + +
89A PHE* 4.3 12.3 - - + -
117A ALA* 3.5 15.0 - - + +
119A ASN 3.1 13.3 + - - +
120A VAL 3.1 8.2 + - - +
122A THR* 1.3 77.4 - - - +
124A ASP* 1.3 64.0 + - - +
126A ILE* 3.2 4.8 + - - +
127A ILE* 3.0 25.8 + - - +
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Residues in contact with ASP 124 (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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29A TRP* 2.7 31.9 + - - -
32A ARG* 4.9 3.2 + - - -
33A HIS* 3.6 11.6 + - - -
120A VAL* 2.8 32.6 + - - +
121A ALA* 3.7 7.7 - - - +
122A THR 3.3 0.2 - - - -
123A ALA* 1.3 73.8 - - - +
125A PHE* 1.3 65.8 + - + +
127A ILE* 3.3 6.0 - - - +
128A GLN* 3.0 48.3 + - - +
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Residues in contact with PHE 125 (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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121A ALA* 3.1 29.3 + - + +
122A THR* 3.7 5.8 - - - +
123A ALA 3.2 0.4 - - - -
124A ASP* 1.3 82.3 - - + +
126A ILE* 1.3 60.8 + - - +
128A GLN* 4.6 3.1 - - - -
129A SER* 3.1 10.6 + - - -
8B LEU* 4.7 7.0 - - + -
12B LYS* 4.8 4.0 - - - -
85B VAL* 6.0 0.7 - - + -
115B PRO* 4.0 24.2 - - + -
125B PHE 4.1 1.7 - - - +
126B ILE* 3.7 28.0 - - + -
129B SER* 2.6 41.3 + - - -
131B HIS* 4.1 19.5 - - + -
132B PHE* 3.9 33.0 - + - -
136B VAL* 4.4 21.5 - - + -
138B ILE* 5.6 2.2 - - + -
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Residues in contact with ILE 126 (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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85A VAL* 4.8 6.5 - - + -
87A ILE* 5.3 5.2 - - + -
115A PRO* 4.3 13.0 - - + -
116A VAL 3.9 24.9 - - - +
117A ALA* 3.8 21.5 - - + -
122A THR* 3.0 23.4 + - + +
123A ALA* 3.8 3.8 - - - +
125A PHE* 1.3 75.7 - - - +
127A ILE* 1.3 61.9 + - - +
129A SER* 3.3 16.4 + - - -
132A PHE* 3.4 26.7 - - + +
122B THR* 4.3 8.5 - - + -
125B PHE* 3.7 34.4 - - + -
126B ILE* 5.0 3.6 - - + -
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Residues in contact with ILE 127 (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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29A TRP* 3.8 28.0 - - + -
33A HIS* 3.9 37.7 - - + +
36A LEU* 3.2 37.8 - - + +
37A LEU* 4.2 13.7 - - + -
123A ALA 3.0 15.5 + - - +
124A ASP* 3.3 17.3 - - - +
126A ILE* 1.3 78.5 - - - +
128A GLN* 1.3 65.9 + - + +
129A SER 3.3 1.1 + - - +
132A PHE* 4.0 27.4 - - + +
133A ASN* 5.3 1.7 + - - -
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Residues in contact with GLN 128 (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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33A HIS* 5.4 6.2 - - + -
124A ASP* 3.0 44.5 + - - +
125A PHE* 5.2 2.4 - - - -
127A ILE* 1.3 82.7 - - + +
129A SER* 1.3 65.2 + - - +
130A PRO* 3.5 1.4 - - - +
129B SER* 3.8 11.7 + - - +
130B PRO* 3.2 24.4 - - + +
131B HIS* 3.5 34.0 + - - +
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Residues in contact with SER 129 (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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125A PHE 3.1 9.2 + - - -
126A ILE 3.3 14.8 - - - -
127A ILE 3.3 1.5 - - - +
128A GLN* 1.3 79.2 - - - +
130A PRO* 1.3 77.8 - - - +
131A HIS* 3.4 1.9 + - - +
132A PHE* 3.2 17.7 + - - +
133A ASN* 5.4 1.0 + - - -
125B PHE* 2.7 47.7 + - - -
128B GLN* 3.8 6.6 + - - +
129B SER* 3.8 6.1 + - - -
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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