Contacts of the helix formed by residues 135 - 154 (chain D) in PDB entry 1P7L
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 PRO 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D TYR* 4.1 16.8 - - + -
127D THR* 3.4 9.6 - - + -
129D GLU* 3.6 7.9 - - - +
133D LEU 4.7 0.2 - - - +
134D MET* 1.3 106.7 - - + +
136D ALA* 1.3 60.6 + - - +
137D PRO* 4.3 3.6 - - + -
138D ILE* 3.6 9.5 - - + +
139D THR* 2.8 24.9 - - - +
251D TYR* 4.0 23.6 - - + +
254D MET* 4.1 31.6 - - + -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU* 2.6 27.7 + - + +
130D THR* 4.2 11.7 - - + -
134D MET 3.6 0.8 + - - -
135D PRO* 1.3 69.7 - - - +
137D PRO* 1.3 70.4 - - + +
139D THR* 2.3 29.3 + - - +
140D TYR* 3.0 27.2 + - + -
170D PHE* 4.2 8.7 - - + -
172D TYR* 4.4 1.3 - - - +
177D ILE* 4.5 9.0 - - + -
215D TRP* 5.1 2.5 - - + -
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Residues in contact with PRO 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PHE* 3.9 21.8 - - + -
7D SER* 3.6 26.5 - - - +
129D GLU* 3.7 0.2 - - - +
135D PRO* 3.8 8.1 - - + -
136D ALA* 1.3 91.9 - - + +
138D ILE* 1.3 62.3 + - - +
140D TYR* 3.4 1.9 + - - +
141D ALA* 3.1 23.7 + - - +
168D VAL* 5.0 2.1 - - - +
170D PHE* 3.3 36.0 - - + -
172D TYR* 3.4 25.1 - - + +
254D MET* 4.4 1.6 - - + -
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D SER* 4.0 5.2 + - - -
8D GLU 3.7 24.7 - - - +
9D SER* 4.6 0.9 - - - +
134D MET* 3.9 23.8 - - + -
135D PRO* 3.6 22.6 - - + +
137D PRO* 1.3 79.7 - - - +
139D THR* 1.3 68.4 + - + +
141D ALA* 3.4 1.5 + - + -
142D HIS* 3.0 52.1 + - + +
248D VAL* 3.8 12.3 - - - +
250D THR 4.5 4.5 - - - +
251D TYR 3.9 8.7 + - - +
252D GLY* 3.7 30.5 - - - +
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Residues in contact with THR 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 4.8 8.0 - - + +
132D VAL* 4.8 5.8 - - + -
134D MET* 3.7 24.0 - - + +
135D PRO 2.8 22.2 - - - +
136D ALA* 2.3 32.8 + - - -
138D ILE* 1.3 81.9 - - + +
140D TYR* 1.3 66.2 + - - +
142D HIS* 3.7 7.1 + - - +
143D ARG* 2.8 43.4 + - - +
361D GLY* 6.3 0.4 - - - -
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Residues in contact with TYR 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 5.9 2.9 - - + +
136D ALA* 3.0 27.8 + - + +
137D PRO 4.2 0.9 - - - +
139D THR* 1.3 86.5 + - - +
141D ALA* 1.3 60.1 + - - +
143D ARG* 3.2 39.7 + - - +
144D LEU* 2.9 33.7 + - - +
168D VAL* 5.3 2.7 - - + -
170D PHE* 3.5 25.4 - + + -
180D ILE* 6.1 0.2 - - + -
210D ILE* 4.1 15.7 - - + +
211D LEU* 4.3 13.7 - - + -
212D PRO* 4.0 20.3 - - + +
215D TRP* 3.2 34.9 - + - -
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D SER 4.8 1.8 - - - -
8D GLU* 3.9 13.7 - - - +
9D SER* 3.6 25.5 - - - +
137D PRO 3.1 17.3 + - - +
138D ILE* 3.8 4.5 - - - +
140D TYR* 1.3 75.8 - - - +
142D HIS* 1.3 64.6 + - - +
144D LEU* 3.0 16.7 + - - -
145D VAL 3.2 4.7 + - - -
166D SER* 3.0 24.4 + - - +
168D VAL* 4.5 10.0 - - + +
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Residues in contact with HIS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 2.4 30.6 + - - -
10D VAL 5.9 0.2 - - - -
134D MET* 6.2 1.3 - - + -
138D ILE* 3.0 35.9 + - + +
139D THR* 3.8 6.7 - - - +
141D ALA* 1.3 75.3 - - - +
143D ARG* 1.3 64.1 + - + +
145D VAL* 3.2 6.7 - - - +
146D GLN* 2.9 33.2 + - - +
248D VAL* 3.0 32.4 + - + -
250D THR 5.5 1.0 + - - -
357D TYR* 3.4 26.6 - - - +
358D GLY* 3.1 28.3 - - - -
360D PHE 5.3 4.5 - - - -
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Residues in contact with ARG 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D VAL* 6.3 1.0 - - - +
139D THR* 2.8 32.0 + - - +
140D TYR* 3.2 42.1 + - - +
141D ALA 3.2 0.4 - - - -
142D HIS* 1.3 77.1 - - + +
144D LEU* 1.3 57.6 + - - +
146D GLN* 3.7 12.1 - - - +
147D ARG* 2.9 30.1 + - - +
210D ILE* 3.7 28.5 + - + +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TYR 2.9 16.8 + - - +
141D ALA 3.0 6.9 + - - +
143D ARG* 1.3 75.8 - - - +
145D VAL* 1.3 66.1 + - - +
147D ARG* 3.3 3.0 + - - -
148D GLN* 3.1 18.2 + - - +
166D SER* 3.9 18.2 - - - +
168D VAL* 3.4 33.7 - - + -
183D VAL* 5.3 4.0 - - + -
184D VAL 5.1 2.2 - - - +
185D LEU* 4.1 11.4 - - + +
206D ILE* 3.5 35.1 - - - +
207D ILE* 4.0 19.3 - - + -
210D ILE* 3.6 16.2 - - + -
211D LEU* 4.1 14.1 - - + -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D SER* 3.7 6.3 - - - +
10D VAL 3.6 19.1 - - - +
11D SER* 3.5 27.2 - - - +
141D ALA 3.2 6.0 + - - +
142D HIS* 3.2 16.6 - - - +
144D LEU* 1.3 78.4 - - - +
146D GLN* 1.3 65.9 + - - +
148D GLN* 3.4 12.1 + - - +
149D ALA* 3.0 21.7 + - - +
164D ALA* 4.2 4.3 - - + +
165D LYS* 4.0 5.6 - - - +
166D SER* 3.6 35.2 - - - +
185D LEU* 5.6 1.6 - - + -
357D TYR* 3.7 12.8 - - + -
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D HIS* 2.9 26.8 + - - +
143D ARG* 3.7 11.4 - - - +
145D VAL* 1.3 75.7 - - - +
147D ARG* 1.3 64.9 + - - +
149D ALA* 3.3 4.8 + - + +
150D GLU* 3.1 22.0 + - - +
357D TYR* 3.6 46.6 + - + +
362D ARG* 5.9 3.2 + - - +
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Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ARG 2.9 19.8 + - - +
144D LEU 3.6 4.5 - - - +
146D GLN* 1.3 74.3 - - - +
148D GLN* 1.3 68.1 + - - +
150D GLU* 2.9 23.0 + - - +
151D VAL* 2.8 33.1 + - + +
154D ASN* 6.2 1.5 - - - +
156D THR* 5.8 0.6 - - - +
205D GLU* 2.6 49.0 + - - +
206D ILE* 3.6 22.7 - - + +
209D PRO* 4.1 17.5 - - - +
210D ILE* 3.8 17.9 - - + -
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Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D SER* 4.0 4.5 - - - -
144D LEU 3.1 9.1 + - - +
145D VAL* 3.4 15.3 - - - +
147D ARG* 1.3 80.1 - - - +
149D ALA* 1.3 83.9 + - - +
151D VAL* 2.9 25.5 - - - +
152D ARG* 3.1 20.4 + - - +
160D LEU* 3.5 11.2 - - + +
161D ARG 3.1 26.5 + - - -
162D PRO 4.0 0.4 + - - -
164D ALA* 3.7 22.9 - - + +
185D LEU* 5.2 4.5 - - + -
187D THR* 3.5 18.8 + - - +
206D ILE* 3.6 26.9 - - + +
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 5.4 0.7 - - - -
12D GLU* 3.6 12.6 - - + +
145D VAL 3.0 6.8 + - - +
146D GLN 3.5 8.3 - - - +
147D ARG 3.1 0.2 - - - -
148D GLN* 1.3 89.7 + - - +
150D GLU* 1.3 56.8 + - - +
152D ARG* 3.3 19.1 + - - +
153D LYS* 3.0 36.1 + - + +
357D TYR* 3.5 25.8 - - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D GLN 3.1 12.1 + - - +
147D ARG* 2.9 27.9 + - - +
149D ALA* 1.3 74.0 - - - +
151D VAL* 1.3 59.6 + - - +
152D ARG 3.0 5.4 - - - -
153D LYS* 4.2 7.2 - - - +
154D ASN* 3.0 45.1 + - - +
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Residues in contact with VAL 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ARG* 2.8 29.0 + - + +
148D GLN* 2.9 32.8 - - - +
150D GLU* 1.3 78.8 - - - +
152D ARG* 1.3 57.2 + - - +
154D ASN* 2.8 22.4 - - - +
156D THR* 3.0 31.6 + - + -
157D LEU* 3.0 31.4 + - + -
160D LEU* 3.6 12.1 - - + -
205D GLU* 3.7 9.2 - - + -
206D ILE* 4.2 10.8 - - + -
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Residues in contact with ARG 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 5.2 0.4 + - - -
12D GLU* 4.5 8.5 - - - +
75D ILE 2.9 27.9 + - - -
76D GLY* 4.6 2.6 - - - -
148D GLN* 3.1 35.1 + - - +
149D ALA* 3.3 20.6 + - - +
151D VAL* 1.3 78.0 - - - +
153D LYS* 1.3 90.1 + - - +
155D GLY* 3.1 14.0 + - - -
157D LEU 4.0 10.5 - - - +
158D PRO* 4.9 3.7 - - - +
160D LEU* 3.5 37.9 - - + +
161D ARG 3.6 14.1 - - - -
162D PRO* 3.4 31.4 + - - +
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 2.6 39.7 + - - +
74D GLU 3.8 17.1 + - - +
149D ALA* 3.0 27.5 + - + +
150D GLU* 4.2 5.6 - - - +
152D ARG* 1.3 94.6 - - - +
154D ASN* 1.3 61.2 + - - +
155D GLY* 3.0 1.8 + - - -
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Residues in contact with ASN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ARG* 6.2 1.4 - - - +
150D GLU* 3.0 35.4 + - - +
151D VAL* 2.8 16.7 - - - +
153D LYS* 1.3 75.6 - - - +
155D GLY* 1.3 59.5 + - - +
156D THR* 2.6 46.1 + - - -
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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