Contacts of the helix formed by residues 127 - 137 (chain A) in PDB entry 3K9O
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 ASP 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A PRO 3.1 6.5 + - - +
84A ILE 3.6 17.5 - - - +
85A SER* 3.8 6.9 + - - -
86A SER* 2.6 38.6 + - - -
87A VAL* 4.5 1.2 + - - +
125A PRO* 3.5 0.9 - - - -
126A GLN* 1.3 79.0 - - - +
128A ALA* 1.3 57.8 + - - +
129A VAL* 3.2 12.8 + - - +
130A VAL* 3.2 30.1 + - + +
131A ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 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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125A PRO* 5.0 7.8 - - + +
126A GLN 4.0 2.6 + - - -
127A ASP* 1.3 69.3 + - - +
129A VAL* 1.3 62.2 + - + +
131A ALA* 3.9 6.2 - - - +
132A ASN* 2.9 31.5 + - - +
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Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 4.3 7.4 - - + -
86A SER* 5.9 0.4 - - - +
127A ASP* 3.2 9.9 + - - +
128A ALA* 1.3 80.8 - - + +
130A VAL* 1.3 63.3 + - - +
132A ASN* 3.4 5.4 + - - +
133A GLN* 3.1 22.5 + - + +
184A SER 5.2 0.2 - - - +
185A SER* 3.8 45.1 - - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TRP* 3.6 45.3 - - + +
81A HIS 3.4 39.0 - - - +
82A PRO 3.6 0.7 - - - -
86A SER* 4.1 2.9 - - - -
127A ASP* 3.2 29.3 + - + +
129A VAL* 1.3 75.6 - - + +
131A ALA* 1.3 60.2 + - - +
133A GLN* 3.3 3.4 + - - +
134A TYR* 2.9 27.2 + - - +
141A PHE* 3.5 22.2 - - + -
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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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82A PRO* 3.9 16.7 - - + +
122A PRO* 4.4 4.9 - - + +
125A PRO* 3.6 27.1 - - + -
127A ASP 3.0 17.6 + - - +
128A ALA* 3.9 4.7 - - - +
130A VAL* 1.3 75.4 - - - +
132A ASN* 1.3 64.5 + - - +
134A TYR* 3.3 4.9 + - - +
135A LYS* 3.2 41.3 + - - +
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Residues in contact with ASN 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 ALA 2.9 20.6 + - - +
129A VAL* 3.6 6.0 + - - +
131A ALA* 1.3 76.9 - - - +
133A GLN* 1.3 58.9 + - - +
135A LYS* 3.3 12.8 + - - +
136A GLN* 2.8 57.6 + - - +
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Residues in contact with GLN 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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80A TRP* 2.8 29.7 + - + -
129A VAL* 3.1 14.6 + - + +
130A VAL* 3.7 7.6 - - - +
132A ASN* 1.3 80.0 - - - +
134A TYR* 1.3 59.7 + - - +
136A GLN* 4.4 1.6 - - - +
137A ASN* 2.8 43.7 + - + +
140A MET* 3.7 31.4 - - + +
141A PHE* 3.2 26.5 - - - +
144A THR* 3.7 6.0 + - - -
184A SER* 3.1 26.7 + - - +
187A SER* 4.9 3.2 + - - +
188A TRP* 5.0 0.2 - - - +
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Residues in contact with TYR 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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82A PRO* 3.6 17.9 - - + -
119A ALA* 5.6 0.5 - - - -
120A ALA* 3.8 30.7 + - + +
122A PRO* 3.8 32.9 - - + +
130A VAL 2.9 14.1 + - - +
131A ALA* 3.4 9.2 - - - +
133A GLN* 1.3 77.4 - - - +
135A LYS* 1.3 64.8 + - + +
138A PRO* 3.7 21.1 - - - +
141A PHE* 3.5 45.0 - + + +
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Residues in contact with LYS 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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122A PRO* 4.0 29.7 + - + +
123A ASP* 6.0 1.8 - - - +
125A PRO* 5.9 0.6 - - - +
131A ALA* 3.2 29.5 + - - +
132A ASN* 3.8 10.4 - - - +
133A GLN 3.1 0.6 - - - -
134A TYR* 1.3 90.5 - - + +
136A GLN* 1.3 71.9 + - + +
138A PRO* 3.6 10.9 - - - +
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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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132A ASN* 2.8 46.1 + - - +
133A GLN* 4.7 1.6 - - - -
135A LYS* 1.3 86.6 - - + +
137A ASN* 1.3 63.0 + - + +
138A PRO* 3.6 3.5 - - - +
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Residues in contact with ASN 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 GLN* 2.8 19.2 + - + +
136A GLN* 1.3 83.0 - - + +
138A PRO* 1.3 67.0 - - - +
139A GLU* 3.6 8.7 + - - +
140A MET* 3.0 51.9 + - + +
141A PHE 2.9 18.5 + - - -
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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