Contacts of the helix formed by residues 124 - 132 (chain A) in PDB entry 3KSA
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 6.0 0.2 - - - -
55A PHE* 3.6 7.6 + - - +
97A ILE* 2.9 33.9 + - - -
98A LEU* 3.2 20.8 + - - -
99A VAL* 4.1 2.2 - - - +
100A GLU* 3.4 19.1 - - - -
122A ARG 3.8 1.0 + - - -
123A LEU* 1.3 80.6 - - - +
125A GLU* 1.3 65.7 + - - +
126A ILE* 3.9 2.2 - - - +
127A ALA* 3.4 18.4 + - - +
128A GLY* 3.9 3.1 + - - -
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Residues in contact with GLU 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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55A PHE* 3.1 50.6 - - + +
100A GLU* 4.2 2.4 + - - +
124A SER* 1.3 75.5 - - - +
126A ILE* 1.3 66.1 + - - +
127A ALA 3.0 1.8 - - - -
128A GLY* 3.0 16.6 + - - -
129A TYR* 3.9 10.6 + - + -
473A LYS* 5.8 3.7 - - - +
474A PHE* 4.1 19.7 - - + -
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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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96A GLU* 3.9 20.0 - - + -
97A ILE 3.9 21.3 - - - +
98A LEU* 4.5 5.4 - - + -
124A SER* 3.9 1.1 - - - +
125A GLU* 1.3 78.5 - - - +
127A ALA* 1.3 66.1 + - - +
128A GLY 3.1 0.2 - - - -
129A TYR* 3.0 18.1 + - + +
130A LEU 3.4 4.0 + - - -
159A PHE* 3.4 31.8 - - + -
183A LEU* 3.5 28.7 - - + -
470A VAL* 5.6 0.4 - - + -
474A PHE* 3.3 53.6 - - + -
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Residues in contact with ALA 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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45A LEU* 4.0 17.9 - - + +
98A LEU* 3.7 20.0 - - + +
123A LEU* 4.2 7.0 - - + -
124A SER* 3.4 26.2 + - - +
125A GLU 3.0 0.8 - - - -
126A ILE* 1.3 80.9 - - - +
128A GLY* 1.3 65.8 + - - +
130A LEU* 2.9 27.9 + - - +
131A LEU* 3.2 11.4 + - - +
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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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49A ASN* 5.8 1.8 - - - -
54A THR* 6.5 1.6 - - - -
123A LEU* 5.7 1.3 - - - +
124A SER 3.9 3.0 + - - -
125A GLU 3.0 11.5 + - - -
127A ALA* 1.3 77.9 - - - +
129A TYR* 1.3 52.9 - - - +
131A LEU* 2.9 15.0 + - - +
132A GLN* 2.7 34.5 + - - +
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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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125A GLU* 3.9 16.4 - - + -
126A ILE* 3.0 13.4 + - + +
128A GLY* 1.3 74.8 - - - +
130A LEU* 1.3 64.0 + - - +
132A GLN* 3.3 18.5 + - + +
157A ALA 4.2 0.5 + - - -
158A ALA* 3.1 35.6 + - + +
159A PHE* 4.5 7.4 - - + -
469A GLU 6.0 0.4 - - - -
470A VAL* 3.4 33.4 - - + -
473A LYS* 4.5 11.4 - - + +
474A PHE* 3.8 29.8 - + - -
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Residues in contact with LEU 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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35A ASP* 5.0 4.3 - - + +
37A LEU* 4.1 15.3 - - + -
45A LEU* 4.7 4.9 - - + -
98A LEU* 3.9 20.9 - - + -
126A ILE 3.4 2.5 + - - +
127A ALA* 2.9 14.1 + - - +
129A TYR* 1.3 77.4 - - - +
131A LEU* 1.3 58.0 + - + +
155A LEU* 3.6 13.6 - - + +
156A PRO* 3.2 11.8 - - - +
157A ALA* 2.9 46.1 + - + +
159A PHE* 3.7 35.7 - - + +
161A ASN* 3.7 32.1 - - + +
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Residues in contact with LEU 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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45A LEU* 3.9 8.1 - - + +
46A TYR* 4.1 26.2 - - + +
49A ASN* 3.2 44.9 - - + +
123A LEU* 3.9 14.4 - - + -
127A ALA 3.2 14.6 + - - +
128A GLY* 2.9 10.1 + - - +
130A LEU* 1.3 77.9 - - + +
132A GLN* 1.3 65.6 + - - +
133A ASP 3.2 0.2 + - - -
134A ILE* 2.9 35.6 + - + +
155A LEU* 3.6 31.6 - - + -
156A PRO* 4.0 4.0 - - - -
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Residues in contact with GLN 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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128A GLY 2.7 15.9 + - - +
129A TYR* 3.3 22.7 + - + +
131A LEU* 1.3 70.1 - - - +
133A ASP* 1.3 81.3 + - - +
156A PRO* 3.2 19.1 - - - +
158A ALA* 5.1 4.9 - - + -
353A ARG* 5.2 0.7 + - - -
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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