Contacts of the helix formed by residues 125 - 134 (chain A) in PDB entry 1S3Y
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 GLY 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A THR* 3.2 5.4 + - - -
124A GLY* 1.3 71.8 - - - -
126A ALA* 1.3 58.3 + - - -
127A GLN 3.0 2.2 - - - -
128A LEU 3.5 0.7 - - - -
129A TYR* 2.7 46.0 + - - -
207A NAP 2.8 37.9 - - - -
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Residues in contact with ALA 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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19A ILE* 4.0 10.8 - - + +
125A GLY* 1.3 70.8 - - - +
127A GLN* 1.3 60.1 - - + +
129A TYR* 3.4 13.5 + - - +
130A LYS* 3.0 29.5 + - - +
154A VAL* 3.4 31.2 - - + -
155A PHE 4.1 9.2 - - - +
157A PRO* 4.2 3.3 - - + +
207A NAP 3.0 16.5 + - - +
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Residues in contact with GLN 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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82A ARG* 5.6 3.6 + - - -
126A ALA* 1.3 75.3 - - + +
128A LEU* 1.3 65.7 + - - +
130A LYS* 3.0 32.8 + - + +
131A ALA* 3.1 7.8 + - - +
207A NAP 3.1 81.0 + - + +
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Residues in contact with LEU 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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56A LEU* 3.7 13.9 - - + +
57A MET* 3.5 29.8 - - - +
58A GLY* 4.2 4.9 - - - +
80A ILE* 4.4 15.5 - - + -
98A LEU* 3.9 27.4 - - + -
122A VAL* 3.9 12.8 - - + -
124A GLY 3.3 26.9 - - - +
125A GLY* 3.0 4.4 + - - +
127A GLN* 1.3 77.6 - - - +
129A TYR* 1.3 57.9 + - - +
131A ALA* 3.3 9.7 + - + +
132A ALA* 2.9 26.9 + - - +
207A NAP 3.7 18.4 + - - +
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Residues in contact with TYR 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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9A LEU* 3.5 31.9 - - + -
10A ILE 2.9 12.1 + - - -
11A VAL* 3.4 24.3 - - + +
19A ILE* 4.0 11.9 - - + -
122A VAL* 3.8 21.3 - - + -
123A ILE 2.6 30.2 + - - -
124A GLY* 3.8 3.9 - - - -
125A GLY 2.7 34.2 + - - +
126A ALA* 3.5 10.8 - - - +
128A LEU* 1.3 74.0 - - - +
130A LYS* 1.3 52.5 + - - +
132A ALA* 3.1 4.5 + - - +
133A MET* 2.7 37.9 + - - +
156A PHE* 3.7 23.8 - + + -
157A PRO* 4.1 8.1 - - + -
207A NAP 5.7 1.6 - - - -
208A TQT 3.5 2.1 + - - -
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Residues in contact with LYS 130 (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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126A ALA* 3.0 23.4 + - + +
127A GLN* 3.0 22.1 + - + +
129A TYR* 1.3 78.5 - - - +
131A ALA* 1.3 62.4 + - - +
133A MET* 3.4 3.7 + - - +
134A ASP* 3.3 27.8 + - - +
157A PRO* 3.8 28.0 - - + +
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Residues in contact with ALA 131 (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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98A LEU* 4.0 14.7 - - + +
127A GLN 3.1 7.2 + - - +
128A LEU* 3.6 15.5 - - + +
130A LYS* 1.3 78.9 - - - +
132A ALA* 1.3 62.8 + - - +
134A ASP* 3.4 7.8 + - - +
135A HIS* 3.2 18.9 + - - +
207A NAP 4.1 20.9 - - - +
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Residues in contact with ALA 132 (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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7A LEU* 5.5 0.7 - - + -
9A LEU* 4.2 9.9 - - + -
98A LEU* 3.8 13.9 - - + +
122A VAL* 4.1 27.4 - - + -
128A LEU 2.9 17.7 + - - +
129A TYR* 3.4 8.1 - - - +
131A ALA* 1.3 75.1 - - - +
133A MET* 1.3 59.4 + - - +
135A HIS* 2.7 29.5 + - - +
138A LEU* 3.5 17.0 - - + +
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Residues in contact with MET 133 (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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9A LEU* 3.8 21.1 - - + -
129A TYR 2.7 24.5 + - - +
130A LYS* 3.8 6.1 - - - +
132A ALA* 1.3 73.2 - - - +
134A ASP* 1.3 62.4 + - - +
135A HIS 3.5 4.5 + - - +
138A LEU* 4.2 12.8 - - - +
141A ILE* 3.9 25.1 - - + -
156A PHE* 4.0 20.6 - - + -
157A PRO* 4.4 8.1 - - + -
158A LEU* 3.8 48.7 - - + +
160A PHE* 4.7 1.8 - - + -
169A TRP* 4.0 16.5 - - + +
204A ARG* 6.0 0.3 + - - -
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Residues in contact with ASP 134 (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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130A LYS* 3.3 17.5 + - - +
131A ALA* 3.8 6.9 - - - +
132A ALA 3.1 1.0 - - - -
133A MET* 1.3 79.0 - - - +
135A HIS* 1.3 63.6 + - - +
136A PRO* 3.6 5.9 - - - +
158A LEU* 5.7 3.6 - - - +
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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