Contacts of the helix formed by residues 131 - 146 (chain A) in PDB entry 1Z29
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 ASN 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 1.3 73.0 - - - +
132A ALA* 1.3 64.3 + - - +
133A LYS* 2.9 32.1 + - - +
134A ASP* 2.6 39.9 + - - +
135A VAL* 3.0 17.3 + - - +
194A GLU* 3.1 29.6 + - - +
262A GLY 4.7 0.2 - - - +
264A TRP* 3.9 1.0 - - - -
291A PHE* 3.9 20.5 - - + -
292A ARG 4.0 9.2 - - - +
293A SER* 3.5 31.5 + - - +
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Residues in contact with ALA 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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130A ARG 3.3 2.8 + - - -
131A ASN* 1.3 69.5 - - - +
133A LYS* 1.3 60.9 + - - +
135A VAL* 3.6 5.6 - - - +
136A ALA* 2.9 30.3 + - - +
162A PHE* 3.9 7.3 - - + -
172A TRP* 3.7 45.6 - - + -
173A TYR* 4.9 0.4 - - + -
276A PHE* 3.7 22.4 - - + -
280A TYR* 4.2 7.9 + - + -
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASN* 2.9 9.7 + - - +
132A ALA* 1.3 75.2 - - - +
134A ASP* 1.3 63.9 + - - +
136A ALA* 3.3 4.2 + - - +
137A VAL* 3.2 26.7 + - - +
264A TRP* 3.4 55.0 - - + +
268A PHE* 3.8 19.1 - - + -
273A ASN* 2.9 22.0 + - - +
276A PHE* 3.8 27.4 - - + -
277A ASP* 2.9 30.7 + - - -
293A SER* 4.3 9.3 + - - +
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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
----------------------------------------------------------
130A ARG* 3.8 22.4 + - - +
131A ASN* 2.6 33.6 + - - +
133A LYS* 1.3 76.7 - - - +
135A VAL* 1.3 63.2 + - - +
137A VAL* 3.6 4.0 + - - +
138A SER* 3.1 25.8 + - - -
194A GLU* 4.7 0.3 - - - +
257A ARG* 5.1 2.4 + - - -
260A MET 4.2 8.6 - - - +
261A ALA* 3.6 5.0 - - - -
262A GLY 2.8 22.8 + - - -
263A ASP* 3.4 8.5 + - - +
264A TRP* 3.1 32.2 + - - +
2001A A3P 4.7 0.7 + - - -
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Residues in contact with VAL 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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46A TYR* 3.8 12.1 - - + -
47A PRO 3.6 18.6 - - - +
48A LYS* 3.9 11.5 - - - +
49A SER* 3.8 12.6 - - - +
130A ARG* 3.7 29.6 - - + +
131A ASN 3.0 18.3 + - - +
132A ALA* 3.6 9.4 - - - +
134A ASP* 1.3 78.0 - - - +
136A ALA* 1.3 52.7 + - - +
138A SER* 3.2 2.5 + - - -
139A TYR* 2.7 36.5 + - + +
162A PHE* 3.7 20.4 - - + -
172A TRP* 4.0 6.7 - - + +
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Residues in contact with ALA 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 ALA 2.9 17.4 + - - +
133A LYS* 3.3 7.8 + - - +
135A VAL* 1.3 76.0 - - - +
137A VAL* 1.3 57.7 + - - +
139A TYR* 3.2 1.3 + - - -
140A TYR* 2.9 26.0 + - - +
155A TRP* 3.9 17.7 - - + -
158A PHE* 3.5 9.1 - - + -
159A LEU* 4.9 3.1 - - + -
162A PHE* 3.8 35.2 - - + -
268A PHE* 4.7 5.6 - - + -
276A PHE* 5.3 0.4 - - + -
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Residues in contact with VAL 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 LYS 3.2 14.4 + - - +
134A ASP* 4.1 5.8 - - - +
136A ALA* 1.3 74.8 - - - +
138A SER* 1.3 60.0 + - - +
140A TYR* 3.3 1.8 + - - +
141A HIS* 2.7 55.2 + - + +
155A TRP* 3.8 24.5 - - + -
257A ARG* 3.8 15.9 - - - +
263A ASP* 5.1 4.0 - - - +
264A TRP* 4.1 13.7 - - + -
267A THR* 3.9 28.9 - - + +
268A PHE* 4.0 8.3 - - + -
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Residues in contact with SER 138 (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 LYS* 3.4 27.0 - - - +
130A ARG* 4.0 4.0 - - - -
134A ASP 3.1 20.3 + - - -
135A VAL 3.6 3.4 - - - -
137A VAL* 1.3 77.6 - - - +
139A TYR* 1.3 61.1 + - - +
141A HIS* 3.6 2.6 + - - +
142A PHE* 3.2 22.7 + - - +
257A ARG* 4.1 5.8 - - - +
2001A A3P 2.5 43.4 + - - -
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Residues in contact with TYR 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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46A TYR* 3.8 26.5 - + - -
47A PRO* 3.7 24.4 - - + +
48A LYS* 3.8 18.1 - - + +
135A VAL* 2.7 18.2 + - + +
136A ALA* 3.6 5.4 - - - +
138A SER* 1.3 77.0 - - - +
140A TYR* 1.3 59.2 + - - +
142A PHE* 3.3 4.9 + + - -
143A TYR* 2.9 49.5 + + - -
149A TYR* 3.8 19.8 + + - -
158A PHE* 3.9 15.7 - + + -
162A PHE* 4.3 7.9 - + - -
167A VAL* 3.9 9.2 - - + -
168A SER* 2.7 44.0 + - - -
169A TYR* 4.1 0.3 - - - -
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Residues in contact with TYR 140 (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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136A ALA 2.9 15.5 + - - +
137A VAL 3.3 4.5 + - - +
139A TYR* 1.3 78.1 - - - +
141A HIS* 1.3 80.6 + + - +
143A TYR* 3.5 4.0 + - - +
144A HIS* 3.2 50.6 + + - -
152A PRO* 3.9 8.3 - - + -
153A GLY 3.3 23.1 + - - -
154A THR* 3.8 3.9 - - - -
155A TRP* 3.4 47.8 + + + +
158A PHE* 3.6 35.0 - + + -
267A THR* 6.0 1.1 - - + -
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Residues in contact with HIS 141 (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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137A VAL* 2.7 47.1 + - + +
138A SER 4.0 2.2 - - - +
140A TYR* 1.3 93.5 - + - +
142A PHE* 1.3 64.7 + - - +
144A HIS* 3.3 17.4 + - - +
145A MET* 3.3 10.7 + - - +
253A SER* 3.4 30.4 - - - +
257A ARG* 3.5 32.7 + - - -
267A THR* 4.9 7.6 - - + -
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Residues in contact with PHE 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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48A LYS* 3.3 35.0 - - + -
138A SER 3.2 18.9 + - - +
139A TYR* 3.7 7.6 - + - +
140A TYR 3.3 0.2 - - - -
141A HIS* 1.3 71.6 - - - +
143A TYR* 1.3 65.7 + - - +
144A HIS 3.0 2.0 + - - -
145A MET* 3.2 27.9 + - + -
146A ALA* 2.9 37.6 + - + +
149A TYR* 2.9 43.1 - + - -
248A MET* 4.2 14.8 - - + -
255A PHE* 3.4 34.8 - + - -
721A ACY 4.0 20.4 - - + -
1010A CA 4.4 0.4 - - - -
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Residues in contact with TYR 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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9A ARG* 3.2 22.2 + - - -
12A LEU* 4.0 7.8 - - - +
139A TYR* 2.9 47.9 + + - +
140A TYR 3.5 7.6 - - - +
142A PHE* 1.3 75.5 - - - +
144A HIS* 1.3 61.4 + - - +
146A ALA 3.3 6.8 - - - +
149A TYR* 3.5 33.8 - + + +
150A PRO* 3.3 39.0 - - + +
152A PRO* 3.7 26.7 - - + +
158A PHE* 3.8 22.2 - + + -
161A LYS* 6.2 3.6 - - + -
166A GLU 4.7 0.3 + - - -
167A VAL* 3.3 11.6 - - + +
168A SER* 3.0 24.6 + - - -
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Residues in contact with HIS 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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9A ARG* 2.8 26.2 + - - +
140A TYR* 3.2 52.1 + + - -
141A HIS* 3.3 15.0 + - - +
142A PHE 3.0 0.8 - - - -
143A TYR* 1.3 81.0 - - - +
145A MET* 1.3 59.2 + - - +
151A HIS* 3.8 22.9 + + - -
152A PRO* 3.6 19.4 - - + +
153A GLY 4.2 2.0 + - - -
252A ILE* 3.7 29.9 - - + +
253A SER* 5.1 1.6 - - - -
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Residues in contact with MET 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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141A HIS 3.3 8.5 + - - +
142A PHE* 3.5 34.5 - - + +
144A HIS* 1.3 79.4 - - - +
146A ALA* 1.3 79.1 + - - +
147A LYS* 3.3 9.4 + - - +
247A PHE 3.7 0.3 - - - +
248A MET* 3.4 29.6 - - + -
249A ASP* 2.9 35.9 + - - +
250A HIS* 3.9 30.1 - - + +
252A ILE* 4.1 5.1 - - - +
253A SER* 3.3 40.4 - - - +
254A PRO 5.3 0.7 - - - -
255A PHE* 3.9 11.2 - - + +
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Residues in contact with ALA 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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9A ARG* 3.8 0.8 + - - -
142A PHE* 2.9 23.7 + - + +
143A TYR 3.3 11.1 - - - +
145A MET* 1.3 81.7 - - - +
147A LYS* 1.3 58.9 + - - +
148A VAL* 3.2 12.1 + - + +
149A TYR* 3.2 43.8 + - + +
247A PHE 3.6 6.7 - - - +
248A MET* 4.4 7.9 - - + -
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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