Contacts of the helix formed by residues 125 - 135 (chain A) in PDB entry 3K2H
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
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Residue Dist Surf HB Arom Phob DC
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69A THR* 3.0 12.9 + - - -
124A GLY* 1.3 73.1 + - - -
126A SER* 1.3 62.7 + - - -
127A PHE 3.4 1.8 - - - -
128A LEU* 3.2 2.6 + - - +
129A TYR* 2.9 30.0 + - - -
515A NAP 2.9 43.0 + - - -
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Residues in contact with SER 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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23A ILE* 3.4 5.1 - - - +
125A GLY* 1.3 67.9 - - - -
127A PHE* 1.3 57.6 + - - -
129A TYR* 3.8 8.3 - - - +
130A LYS* 2.7 38.7 + - - +
154A THR* 3.1 20.3 - - - +
155A TYR 2.6 29.5 + - - -
157A PRO* 4.6 2.6 - - - +
515A NAP 2.8 16.7 + - - -
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Residues in contact with PHE 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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68A LYS* 4.2 17.5 - - - -
126A SER* 1.3 77.7 - - - +
128A LEU* 1.3 57.5 + - - +
130A LYS* 3.9 4.3 - - - +
131A GLU* 3.0 29.5 + - - +
515A NAP 3.3 83.9 - + + +
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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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64A ILE* 3.7 33.0 - - + +
65A PHE 3.9 0.4 - - - -
66A GLY 3.9 8.3 - - - +
88A LEU* 3.5 24.0 - - + -
104A LEU* 4.0 24.7 - - + -
122A ILE* 3.9 17.9 - - + -
124A GLY 3.6 22.2 - - - +
125A GLY 3.2 9.1 + - - +
126A SER 3.1 0.4 - - - -
127A PHE* 1.3 78.6 - - - +
129A TYR* 1.3 65.9 + - - +
131A GLU* 3.3 3.4 + - - +
132A VAL* 2.9 31.8 + - + +
515A NAP 4.4 13.0 - - + +
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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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13A ILE* 3.6 31.4 - - + -
14A PHE 3.0 16.6 + - - -
15A VAL* 3.4 20.4 - - + +
23A ILE* 3.7 18.6 - - + -
122A ILE* 3.8 10.1 - - + -
123A LEU 3.3 5.7 - - - -
124A GLY* 3.3 27.1 - - - -
125A GLY 2.9 24.0 + - - +
126A SER* 3.8 3.8 - - - +
128A LEU* 1.3 74.8 - - - +
130A LYS* 1.3 57.7 + - - +
132A VAL* 3.3 6.1 + - - +
133A LEU* 2.9 35.8 + - + +
156A PHE* 3.6 28.5 - + + -
157A PRO* 4.0 9.6 - - + -
515A NAP 3.1 22.9 - + - -
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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 SER* 2.7 22.6 + - - +
127A PHE* 3.9 4.9 - - - +
129A TYR* 1.3 70.4 - - - +
131A GLU* 1.3 59.8 + - - +
132A VAL 3.3 0.2 + - - -
133A LEU* 4.8 0.9 - - + -
134A ASP* 2.7 74.1 + - - +
157A PRO* 3.8 28.8 - - + +
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Residues in contact with GLU 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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5A TYR* 2.5 39.5 + - + +
103A ASP* 5.6 1.4 - - - +
104A LEU* 3.7 25.4 + - + +
105A SER 5.0 0.3 + - - -
127A PHE 3.0 17.3 + - - +
128A LEU* 3.9 5.9 - - - +
130A LYS* 1.3 76.8 - - - +
132A VAL* 1.3 62.7 + - - +
134A ASP* 4.7 2.0 - - - -
135A ASN* 3.0 36.5 + - - +
137A LEU* 4.5 0.6 - - + +
515A NAP 2.7 33.0 + - - -
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Residues in contact with VAL 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 LEU* 4.0 18.8 - - + -
13A ILE* 3.8 16.6 - - + -
104A LEU* 3.7 22.7 - - + -
122A ILE* 4.1 16.8 - - + -
128A LEU* 2.9 21.8 + - + +
129A TYR* 3.6 4.7 - - - +
131A GLU* 1.3 78.2 - - - +
133A LEU* 1.3 59.7 + - - +
136A GLY 3.4 1.2 + - - -
137A LEU* 2.9 39.3 + - + +
138A CYS* 3.6 30.8 + - + +
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Residues in contact with LEU 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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13A ILE* 4.3 12.6 - - + -
129A TYR 2.9 20.9 + - - +
130A LYS* 4.0 2.5 - - - +
132A VAL* 1.3 73.3 - - - +
134A ASP* 1.3 67.4 + - - +
135A ASN 3.0 2.0 - - - -
136A GLY* 3.0 14.2 + - - -
138A CYS* 4.5 7.2 - - + -
141A ILE* 4.3 16.4 - - + -
156A PHE* 4.2 22.9 - - + -
157A PRO* 4.0 27.8 - - + -
158A ASP 4.4 9.0 - - - +
159A ILE* 5.3 0.9 - - + -
160A PRO* 4.2 32.2 - - + +
163A PHE* 4.2 16.4 - - + -
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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* 2.7 67.0 + - - +
131A GLU* 4.2 4.0 - - - +
133A LEU* 1.3 73.5 - - - +
135A ASN* 1.3 66.1 + - - +
136A GLY 3.7 0.5 + - - -
157A PRO* 5.8 0.2 - - - +
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Residues in contact with ASN 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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5A TYR* 3.4 45.6 + - + +
131A GLU* 3.0 30.3 + - - +
133A LEU 3.0 0.8 - - - -
134A ASP* 1.3 84.4 - - - +
136A GLY* 1.3 62.0 + - - +
137A LEU* 3.2 23.2 + - + +
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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