Contacts of the helix formed by residues 135 - 154 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TYR* 4.1 22.2 - - + -
126A ALA* 6.4 0.2 - - - -
127A THR* 3.4 8.5 - - + -
129A GLU* 3.6 7.6 - - - +
134A MET* 1.3 106.1 - - + +
136A ALA* 1.3 61.7 + - - +
137A PRO* 4.4 3.4 - - + -
138A ILE* 3.6 10.0 - - + +
139A THR* 2.9 23.9 - - - +
251A TYR* 4.0 23.8 - - + +
254A MET* 4.1 26.2 - - + -
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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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129A GLU* 2.6 26.9 + - + +
130A THR* 4.3 12.3 - - + -
134A MET 3.7 0.4 + - - -
135A PRO* 1.3 70.1 - - - +
137A PRO* 1.3 73.5 - - + +
139A THR* 2.3 30.4 + - - +
140A TYR* 3.1 26.4 + - + -
170A PHE* 4.3 8.3 - - + -
172A TYR* 4.4 1.3 - - - +
177A ILE* 4.6 8.5 - - + -
215A TRP* 5.2 2.2 - - + -
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Residues in contact with PRO 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.9 23.1 - - + -
7A SER* 3.6 25.1 - - - +
129A GLU* 3.8 0.2 - - - +
135A PRO* 3.9 7.4 - - + -
136A ALA* 1.3 93.7 - - + +
138A ILE* 1.3 61.8 + - - +
140A TYR* 3.6 0.9 + - - -
141A ALA* 3.2 23.9 + - - +
168A VAL* 5.0 2.4 - - - +
170A PHE* 3.3 37.7 - - + -
172A TYR* 3.3 23.1 - - + +
254A MET* 4.4 1.6 - - + -
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Residues in contact with ILE 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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7A SER* 3.9 5.4 + - - -
8A GLU 3.5 25.6 - - - +
134A MET* 3.9 23.1 - - + -
135A PRO* 3.6 22.4 - - + +
137A PRO* 1.3 79.3 - - - +
139A THR* 1.3 65.7 + - + +
141A ALA* 3.5 0.8 + - - -
142A HIS* 3.1 51.7 + - + +
248A VAL* 3.8 12.6 - - - +
250A THR 4.6 4.5 - - - +
251A TYR 3.9 9.2 - - - +
252A GLY* 3.7 30.7 - - - +
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Residues in contact with THR 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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130A THR* 4.8 8.8 - - + +
132A VAL* 4.8 6.1 - - + -
134A MET* 3.7 23.3 - - + +
135A PRO 2.9 22.0 - - - +
136A ALA* 2.3 33.5 + - - -
138A ILE* 1.3 80.6 - - + +
140A TYR* 1.3 70.3 + - - -
142A HIS* 3.6 7.3 + - - +
143A ARG* 2.8 43.0 + - - +
361A GLY* 6.2 0.9 - - - -
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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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130A THR* 5.9 3.3 - - + +
136A ALA* 3.1 20.2 + - + +
137A PRO 4.3 0.2 - - - +
139A THR* 1.3 86.7 + - - +
141A ALA* 1.3 61.8 + - - +
143A ARG* 3.3 41.4 + - - +
144A LEU* 2.9 33.4 + - - +
168A VAL* 5.2 2.2 - - + -
170A PHE* 3.4 32.8 - + + -
210A ILE* 4.1 15.3 - - + +
211A LEU* 4.3 15.3 - - + -
212A PRO* 4.1 18.5 - - + +
215A TRP* 3.2 35.5 - + - -
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Residues in contact with ALA 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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7A SER 4.7 1.1 - - - +
8A GLU* 3.9 20.9 - - - +
9A SER* 3.5 14.5 - - - -
137A PRO 3.2 18.6 + - - +
138A ILE* 3.9 4.0 - - - +
140A TYR* 1.3 72.7 - - - +
142A HIS* 1.3 67.1 + - - +
144A LEU* 3.1 15.4 + - - -
145A VAL 3.3 4.5 + - - -
166A SER* 2.9 29.0 + - - +
168A VAL* 4.4 9.3 - - + +
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Residues in contact with HIS 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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9A SER* 2.5 30.2 + - - -
134A MET* 6.1 2.0 - - + +
138A ILE* 3.1 36.7 + - + +
139A THR* 3.7 7.4 - - - +
141A ALA* 1.3 75.3 - - - +
143A ARG* 1.3 64.1 + - + +
145A VAL* 3.1 6.4 - - - +
146A GLN* 2.8 32.4 + - - +
248A VAL* 3.0 35.1 + - + -
250A THR 5.4 1.0 + - - -
357A TYR* 3.4 27.0 - - - +
358A GLY* 3.2 25.8 - - - -
360A PHE 5.4 4.7 - - - -
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Residues in contact with ARG 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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132A VAL* 6.3 0.6 - - - +
139A THR* 2.8 31.1 + - - +
140A TYR* 3.4 45.6 + - - +
141A ALA 3.2 0.2 - - - -
142A HIS* 1.3 77.3 - - + +
144A LEU* 1.3 57.7 + - - +
146A GLN* 3.7 12.5 - - - +
147A ARG* 2.9 31.7 + - - +
210A ILE* 3.7 29.4 + - + +
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Residues in contact with LEU 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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140A TYR 2.9 16.9 + - - +
141A ALA 3.1 6.5 + - - +
143A ARG* 1.3 77.1 - - - +
145A VAL* 1.3 63.7 + - - +
147A ARG* 3.2 1.5 + - - -
148A GLN* 3.1 18.7 + - - +
166A SER* 3.8 18.6 - - - +
168A VAL* 3.4 33.2 - - + -
183A VAL* 5.3 4.5 - - + -
184A VAL 5.1 2.0 - - - +
185A LEU* 4.1 9.4 - - + -
206A ILE* 3.5 31.8 - - + +
207A ILE* 4.0 17.9 - - + -
210A ILE* 3.5 21.3 - - + -
211A LEU* 4.1 15.3 - - + -
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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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9A SER* 4.0 5.2 - - - +
10A VAL* 3.6 21.3 - - - +
11A SER* 3.5 28.3 - - - +
141A ALA 3.7 6.1 - - - +
142A HIS* 3.1 20.6 - - - +
144A LEU* 1.3 79.5 - - - +
146A GLN* 1.3 62.2 + - - +
148A GLN* 3.4 11.4 + - - +
149A ALA* 3.1 23.0 + - - +
164A ALA* 4.1 4.5 - - + +
165A LYS* 4.1 5.4 - - - -
166A SER* 3.7 33.0 - - - +
185A LEU* 5.5 2.5 - - + -
357A TYR* 3.7 13.7 + - + -
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Residues in contact with GLN 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 HIS* 2.8 25.6 + - - +
143A ARG* 3.7 11.2 - - - +
145A VAL* 1.3 80.3 - - - +
147A ARG* 1.3 62.3 + - - +
149A ALA* 3.4 3.1 + - - +
150A GLU* 3.1 22.2 + - - +
357A TYR* 3.6 45.0 + - + +
362A ARG* 5.9 2.6 + - - +
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Residues in contact with ARG 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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143A ARG 2.9 19.5 + - - +
144A LEU 3.5 3.8 - - - +
146A GLN* 1.3 73.9 - - - +
148A GLN* 1.3 67.6 + - - +
150A GLU* 2.9 22.6 + - - +
151A VAL* 2.8 34.7 + - + +
154A ASN* 6.0 2.5 - - - +
156A THR* 5.7 1.2 + - - +
205A GLU* 2.6 47.1 + - - +
206A ILE* 3.6 22.7 - - + +
209A PRO* 4.2 16.6 - - - +
210A ILE* 3.8 19.5 - - + -
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Residues in contact with GLN 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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11A SER* 4.0 4.9 - - - -
144A LEU 3.1 9.5 + - - +
145A VAL* 3.4 13.6 + - - +
147A ARG* 1.3 79.7 - - - +
149A ALA* 1.3 75.8 + - - +
151A VAL* 2.8 25.3 - - - +
152A ARG* 3.1 19.2 + - - +
160A LEU* 3.5 12.5 - - + +
161A ARG 3.0 27.1 + - - -
162A PRO 4.3 0.4 + - - -
164A ALA* 3.7 23.2 - - + +
185A LEU* 5.2 4.5 - - + -
187A THR* 3.3 21.9 + - - +
206A ILE* 3.5 26.7 - - + +
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Residues in contact with ALA 149 (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 SER* 5.4 0.7 - - - -
12A GLU* 3.6 12.6 - - + +
145A VAL 3.1 9.6 + - - +
146A GLN* 3.6 5.8 - - + +
147A ARG 3.1 0.6 - - - -
148A GLN* 1.3 89.3 + - - +
150A GLU* 1.3 57.8 + - - +
152A ARG* 3.4 16.4 + - - +
153A LYS* 3.0 37.0 + - + +
357A TYR* 3.4 25.1 - - + +
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Residues in contact with GLU 150 (chain A).
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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146A GLN 3.1 16.2 + - - +
147A ARG* 2.9 25.9 + - - +
149A ALA* 1.3 74.5 - - - +
151A VAL* 1.3 59.5 + - - +
152A ARG 3.1 4.9 - - - -
153A LYS* 4.1 6.0 - - - +
154A ASN* 3.0 44.8 + - - +
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Residues in contact with VAL 151 (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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147A ARG* 2.8 29.4 + - + +
148A GLN* 2.8 32.8 - - - +
150A GLU* 1.3 78.4 - - - +
152A ARG* 1.3 57.6 + - - +
154A ASN* 2.8 22.4 - - - +
156A THR* 3.1 26.7 + - + +
157A LEU* 2.9 37.9 + - + -
160A LEU* 3.6 11.4 - - + -
205A GLU* 3.8 7.6 - - + -
206A ILE* 4.2 9.6 - - + -
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Residues in contact with ARG 152 (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 SER* 5.2 0.4 + - - -
12A GLU* 4.5 7.5 - - - +
75A ILE 2.7 29.9 + - - -
76A GLY* 4.5 3.0 - - - -
148A GLN* 3.1 23.2 + - - +
149A ALA* 3.5 27.6 + - - +
150A GLU 3.1 0.4 - - - -
151A VAL* 1.3 78.3 - - - +
153A LYS* 1.3 88.3 + - - +
155A GLY* 3.2 12.6 + - - -
157A LEU 4.0 10.8 - - - +
158A PRO* 4.9 4.8 - - - +
160A LEU* 3.4 37.7 - - + +
161A ARG* 3.5 14.8 - - - +
162A PRO* 3.3 35.2 + - - +
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Residues in contact with LYS 153 (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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12A GLU* 2.6 38.9 + - - -
74A GLU 3.9 16.4 + - - +
149A ALA* 3.0 29.1 + - + +
150A GLU* 3.5 5.1 + - - +
152A ARG* 1.3 90.8 - - - +
154A ASN* 1.3 58.6 + - - +
155A GLY* 3.0 10.1 + - - -
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Residues in contact with ASN 154 (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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147A ARG* 6.0 2.4 - - - +
150A GLU* 3.0 36.2 + - - +
151A VAL* 2.8 14.0 - - - +
153A LYS* 1.3 75.3 - - - +
155A GLY* 1.3 59.2 + - - +
156A THR* 2.6 47.2 + - - -
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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