Contacts of the helix formed by residues 134 - 148 (chain A) in PDB entry 2AAK
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 LYS 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A PRO* 5.7 5.4 - - - -
129A MET 3.9 2.4 + - - -
130A TYR* 3.1 45.2 + - - +
132A GLU 4.0 2.0 + - - -
133A SER* 1.3 70.6 - - - +
135A ARG* 1.3 56.7 + - - +
136A GLU 3.4 0.2 - - - -
137A TYR* 3.8 18.6 - - + -
138A ASN* 3.0 54.2 + - - +
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 2.8 8.7 + - - +
134A LYS* 1.3 79.0 - - - +
136A GLU* 1.3 77.6 + - + +
138A ASN* 4.1 5.0 - - - +
139A ARG* 3.5 24.1 + - - +
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Residues in contact with GLU 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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129A MET* 3.8 23.3 - - + +
133A SER* 2.9 29.4 + - - +
135A ARG* 1.3 91.1 + - - +
137A TYR* 1.3 64.4 + - - +
139A ARG* 3.4 10.8 - - + +
140A ARG* 3.1 28.9 + - + +
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Residues in contact with TYR 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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47A PRO* 5.1 7.0 - - + -
48A TRP* 3.9 11.5 + - - -
77A PHE* 4.2 19.3 - + - -
78A HIS* 4.0 6.2 - - - -
79A PRO* 4.1 21.7 - - + +
113A LEU 3.9 17.3 + - - -
114A CYS* 5.5 0.5 - - - -
116A PRO* 4.3 5.5 - - - +
126A ALA 4.3 1.6 - - - -
129A MET* 3.9 27.2 - - - +
130A TYR* 3.6 43.1 - + + -
133A SER 3.5 2.0 + - - -
134A LYS* 3.7 15.7 - - + +
135A ARG 3.3 0.4 - - - -
136A GLU* 1.3 76.0 - - - +
138A ASN* 1.3 74.3 + - - +
140A ARG* 3.2 4.3 + - - +
141A VAL* 2.8 51.5 + - + +
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.8 29.6 - - + +
134A LYS* 3.0 38.7 + - - +
135A ARG* 4.1 5.5 - - - +
137A TYR* 1.3 88.6 - - - +
139A ARG* 1.3 57.8 + - - +
141A VAL* 3.7 7.4 - - - +
142A ARG* 2.9 34.9 + - + +
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Residues in contact with ARG 139 (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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135A ARG* 3.5 15.9 + - - +
136A GLU* 3.4 15.6 + - + +
138A ASN* 1.3 77.9 - - - +
140A ARG* 1.3 67.8 + - + +
142A ARG* 3.3 21.9 - - - +
143A ASP* 3.3 21.8 + - - +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 6.0 1.6 - - - +
77A PHE* 3.5 37.6 - - + +
125A GLU* 3.0 26.1 + - - -
129A MET* 3.4 28.0 - - - +
136A GLU 3.1 15.1 + - - +
137A TYR 3.5 3.6 - - - +
139A ARG* 1.3 81.2 - - + +
141A VAL* 1.3 65.5 + - - +
143A ASP* 3.4 23.1 + - - +
144A VAL* 3.6 11.8 + - - +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PRO* 3.6 24.0 - - + +
48A TRP* 3.5 46.7 - - + +
77A PHE* 4.4 5.4 - - + +
137A TYR* 2.8 54.8 + - + +
138A ASN* 3.7 7.4 - - - +
140A ARG* 1.3 74.5 - - - +
142A ARG* 1.3 65.2 + - - +
143A ASP 3.0 1.2 + - - -
144A VAL* 3.1 13.8 + - - +
145A VAL* 3.1 17.9 + - + +
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Residues in contact with ARG 142 (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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46A THR 4.8 0.2 + - - -
47A PRO* 3.1 26.9 + - + +
49A ASP* 2.7 35.4 + - - +
138A ASN* 2.9 17.7 + - + +
139A ARG* 3.3 15.9 - - - +
141A VAL* 1.3 77.1 - - - +
143A ASP* 1.3 57.4 + - - +
145A VAL* 3.3 22.7 + - - +
146A GLU* 2.9 51.8 + - - +
149A TRP* 4.4 12.7 - - - -
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Residues in contact with ASP 143 (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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139A ARG* 3.3 26.4 + - - +
140A ARG* 3.5 17.9 - - - +
141A VAL 3.0 0.6 + - - -
142A ARG* 1.3 76.2 - - - +
144A VAL* 1.3 66.6 + - + +
145A VAL 3.0 1.6 - - - -
146A GLU* 3.1 11.5 + - - +
147A GLN* 2.9 35.6 + - - +
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Residues in contact with VAL 144 (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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48A TRP* 3.9 24.9 - - + -
53A PHE* 3.7 7.0 - - + -
75A ARG* 3.5 42.6 - - - +
76A MET* 3.8 9.0 - - - -
77A PHE* 3.9 15.3 - - + +
140A ARG 3.6 4.0 + - - +
141A VAL* 3.1 17.5 + - - +
143A ASP* 1.3 77.6 - - + +
145A VAL* 1.3 56.3 + - - +
147A GLN* 3.4 23.4 - - - +
148A SER* 3.1 29.5 + - - -
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Residues in contact with VAL 145 (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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47A PRO 4.1 13.2 - - - +
48A TRP* 3.9 21.5 - - + +
51A GLY 3.9 10.3 - - - +
53A PHE* 3.9 16.6 - - + -
141A VAL* 3.1 19.4 + - + +
142A ARG* 3.3 30.7 - - - +
143A ASP 3.0 0.6 - - - -
144A VAL* 1.3 76.7 - - - +
146A GLU* 1.3 62.0 + - - +
148A SER* 2.8 21.9 + - - -
149A TRP* 3.4 34.8 - - + -
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Residues in contact with GLU 146 (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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142A ARG* 2.9 42.0 + - - +
143A ASP* 3.1 10.2 + - - +
145A VAL* 1.3 77.1 - - + +
147A GLN* 1.3 61.0 + - - +
149A TRP* 3.3 49.1 + - + +
150A THR* 3.9 5.4 + - - -
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Residues in contact with GLN 147 (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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75A ARG* 4.2 26.8 - - + +
143A ASP* 2.9 26.4 + - - +
144A VAL* 3.4 37.0 - - - +
146A GLU* 1.3 73.7 - - - +
148A SER* 1.3 61.4 + - - +
149A TRP 3.1 2.4 + - - -
150A THR* 3.5 23.5 + - - +
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Residues in contact with SER 148 (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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51A GLY* 3.9 0.2 - - - -
52A THR* 3.3 44.2 + - - +
53A PHE* 3.8 16.3 - - - -
74A SER* 4.6 14.1 - - - -
75A ARG 5.7 0.2 - - - -
144A VAL 3.1 16.4 + - - -
145A VAL 2.8 19.9 + - - -
147A GLN* 1.3 76.9 - - - +
149A TRP* 1.3 63.2 + - - +
150A THR 3.2 3.5 + - - -
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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