Contacts of the helix formed by residues 127 - 137 (chain A) in PDB entry 3K9W
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ARG* 5.1 0.9 - - - +
125A PHE 3.5 5.0 + - - -
126A ILE* 1.3 75.0 - - - +
128A GLY* 1.3 59.4 + - - +
129A THR* 3.3 7.1 + - - -
130A ILE* 3.2 40.8 + - - +
131A VAL* 2.9 31.3 + - - +
170A ACT 3.5 22.7 - - - +
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Residues in contact with GLY 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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11A ASP 5.2 2.5 - - - -
12A PRO* 5.1 2.0 - - - +
14A THR* 4.5 14.6 - - - +
17A HIS* 6.1 1.8 - - - -
126A ILE* 4.2 2.2 + - - +
127A SER* 1.3 71.7 - - - +
129A THR* 1.3 57.1 + - - +
131A VAL* 3.2 10.1 + - - +
132A ARG* 2.9 45.2 + - - +
168A ADE 5.3 0.6 + - - -
170A ACT 3.1 17.0 + - - -
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Residues in contact with THR 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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127A SER* 3.2 7.4 - - - -
128A GLY* 1.3 76.2 - - - +
130A ILE* 1.3 61.4 + - + +
132A ARG* 3.3 28.7 + - - +
133A GLU* 3.1 31.3 + - - +
170A ACT 3.1 18.6 + - - +
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Residues in contact with ILE 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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125A PHE 6.0 0.9 - - - +
127A SER* 3.2 28.7 + - - +
129A THR* 1.3 76.9 - - + +
131A VAL* 1.3 60.8 + - + +
133A GLU* 3.3 16.3 + - + +
134A ILE* 2.9 49.2 + - + +
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Residues in contact with VAL 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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12A PRO* 4.7 8.7 - - + -
14A THR* 4.7 2.2 - - + -
126A ILE* 4.0 12.1 - - + -
127A SER 2.9 19.4 + - - +
128A GLY* 3.4 11.7 - - - +
130A ILE* 1.3 78.0 - - + +
132A ARG* 1.3 62.9 + - - +
134A ILE* 3.4 2.2 + - - -
135A ALA* 3.0 22.5 + - - +
141A VAL* 3.5 20.4 - - + +
144A PHE* 3.7 32.5 - - + -
145A VAL* 3.9 24.2 - - + -
153A LEU* 4.2 11.9 - - + -
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Residues in contact with ARG 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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11A ASP* 2.8 59.3 + - - +
12A PRO* 4.3 8.7 - - + -
44A PHE* 3.7 25.0 - - + +
128A GLY* 2.9 25.9 + - - +
129A THR* 3.3 36.9 + - - +
130A ILE 3.3 0.2 - - - -
131A VAL* 1.3 75.7 - - - +
133A GLU* 1.3 57.5 + - - +
135A ALA* 3.2 6.2 + - - +
136A GLN* 2.9 49.4 + - - +
153A LEU* 4.9 5.4 - - + -
170A ACT 5.1 1.6 + - - -
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Residues in contact with GLU 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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129A THR* 3.1 18.7 + - - +
130A ILE* 3.3 21.4 + - - +
132A ARG* 1.3 76.1 - - - +
134A ILE* 1.3 65.5 + - + +
136A GLN* 3.4 11.9 + - - +
137A LEU* 3.1 43.7 + - + +
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Residues in contact with ILE 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 ILE* 2.9 39.8 + - + +
133A GLU* 1.3 76.9 - - + +
135A ALA* 1.3 61.1 + - - +
137A LEU* 3.2 14.4 + - - +
138A GLY 3.2 0.2 + - - -
139A GLY* 2.8 43.7 + - - -
140A ASP 4.0 5.6 - - - +
141A VAL* 3.6 21.1 - - + -
144A PHE* 4.1 24.7 - - + -
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Residues in contact with ALA 135 (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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44A PHE* 6.1 0.2 - - + -
131A VAL 3.0 17.2 + - - +
132A ARG 3.7 3.8 - - - +
134A ILE* 1.3 76.4 - - - +
136A GLN* 1.3 58.8 + - + +
138A GLY* 3.0 19.6 + - - -
139A GLY 3.8 11.0 - - - +
141A VAL* 4.1 6.3 - - + +
150A GLU* 5.6 1.3 - - - +
153A LEU* 4.0 39.0 - - + -
157A VAL* 3.6 18.3 - - + +
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Residues in contact with GLN 136 (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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44A PHE* 3.4 39.7 - - + +
132A ARG* 2.9 35.9 + - - +
133A GLU* 3.8 9.0 - - - +
134A ILE 3.3 0.2 - - - -
135A ALA* 1.3 77.3 - - - +
137A LEU* 1.3 63.7 + - + +
138A GLY 3.2 1.1 + - - -
157A VAL* 3.9 28.3 - - + +
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Residues in contact with LEU 137 (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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133A GLU* 3.1 35.6 + - + +
134A ILE* 3.2 6.2 + - - +
136A GLN* 1.3 81.6 - - + +
138A GLY* 1.3 60.1 + - - +
139A GLY* 3.4 2.0 - - - +
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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