Contacts of the helix formed by residues 132 - 147 (chain B) in PDB entry 1PJS
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 SER 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 5.0 0.4 - - - -
158A ALA* 3.9 13.0 - - - -
179A TRP* 5.3 3.3 - - - -
183A PHE* 3.1 26.9 - - - -
128B SEP 3.1 18.0 - - - -
131B THR* 1.3 87.2 + - - +
133B PRO* 1.3 66.1 - - - +
134B VAL* 3.4 8.3 + - - +
135B LEU* 3.1 30.0 + - - +
136B ALA 3.2 4.9 + - - -
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Residues in contact with PRO 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ARG* 3.5 36.3 - - - +
262A ASP* 6.0 1.6 - - - +
128B SEP 3.3 28.7 - - - +
130B GLY 5.2 0.4 - - - +
131B THR 4.0 0.4 - - - +
132B SER* 1.3 85.5 - - - +
134B VAL* 1.3 68.5 + - + +
136B ALA* 3.1 4.0 + - + +
137B ARG* 3.0 39.1 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG* 5.9 3.6 - - + -
179A TRP* 3.7 36.8 - - + +
180A GLU* 5.4 4.3 - - + +
183A PHE* 3.6 20.9 - - + -
132B SER* 3.0 9.6 - - - +
133B PRO* 1.3 84.1 - - + +
135B LEU* 1.3 62.3 + - - +
137B ARG* 3.3 30.5 + - - +
138B LEU* 3.0 36.7 + - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 4.1 20.4 - - + -
151A LEU* 4.6 14.4 - - + +
154A VAL* 5.6 0.9 - - + -
155A ALA* 3.7 34.1 - - + +
183A PHE* 3.7 18.4 - - + -
506A PGE 4.0 26.5 - - - +
128B SEP 6.0 0.2 - - - -
131B THR* 5.8 0.2 - - - +
132B SER* 3.1 20.3 + - - +
134B VAL* 1.3 80.0 - - - +
136B ALA* 1.3 64.0 + - - +
138B LEU* 3.1 11.3 + - + -
139B LEU* 2.9 37.7 + - + +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 5.4 2.5 - - - -
115B SER* 3.8 18.5 - - - +
126B VAL* 4.3 14.2 - - - +
128B SEP 2.9 35.6 - - - +
132B SER 3.2 4.2 + - - +
133B PRO 3.1 10.6 + - - +
135B LEU* 1.3 79.3 - - - +
137B ARG* 1.3 56.8 + - - +
139B LEU* 3.2 9.2 + - - +
140B ARG* 2.9 27.9 + - - +
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ARG* 3.7 24.9 - - - +
240A GLN* 3.7 13.5 - - - +
241A GLN* 4.3 10.9 - - + +
260A ARG* 3.6 51.9 - - - +
262A ASP* 5.0 2.0 + - - -
115B SER* 4.9 1.1 - - - +
133B PRO* 3.0 22.2 + - - +
134B VAL* 3.6 43.5 - - - +
136B ALA* 1.3 72.8 - - - +
138B LEU* 1.3 60.9 + - - +
140B ARG* 3.7 2.4 - - - +
141B GLU* 2.9 32.1 + - - +
507B PO4 3.1 30.0 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PHE* 3.9 23.6 - - + +
241A GLN* 5.1 11.7 - - - +
506A PGE 4.8 16.6 - - - +
134B VAL* 3.0 39.9 + - + +
135B LEU* 3.3 25.8 - - + +
137B ARG* 1.3 75.5 - - + +
139B LEU* 1.3 62.4 + - - +
141B GLU* 3.7 12.7 + - - +
142B LYS* 3.2 33.7 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.6 34.5 - - + -
124A VAL* 4.5 0.9 - - + -
146A LEU* 5.5 1.6 - - + -
147A LEU* 3.7 23.3 - - + -
151A LEU* 4.5 2.5 - - + -
506A PGE 3.3 33.0 - - - +
126B VAL* 3.4 31.9 - - + -
135B LEU* 2.9 21.3 + - + +
136B ALA* 3.6 7.4 - - - +
138B LEU* 1.3 76.1 - - - +
140B ARG* 1.3 65.4 + - - +
142B LYS* 3.2 6.0 + - + +
143B LEU* 2.8 35.5 + - + +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A GLN* 3.4 26.1 + - - +
257A ASN 3.1 26.7 + - - -
258A LEU* 4.1 1.0 - - - +
259A VAL 3.3 16.6 + - - -
260A ARG* 3.9 2.4 - - - +
261A ARG* 3.1 24.1 - - - +
115B SER* 4.3 11.7 - - - -
116B ILE 3.3 11.1 + - - +
117B ILE* 3.5 24.8 - - + +
126B VAL* 4.2 2.3 - - + +
136B ALA 2.9 16.0 + - - +
137B ARG* 3.2 6.5 + - - +
139B LEU* 1.3 75.0 - - - +
141B GLU* 1.3 53.6 + - - +
143B LEU 3.1 0.7 + - - -
144B GLU* 2.8 61.1 + - + +
507B PO4 2.5 43.4 + - - -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU 5.1 1.3 - - - +
236A LEU* 3.5 14.2 - - + +
237A GLN* 3.6 38.3 + - - +
240A GLN* 3.5 33.9 + - + +
241A GLN* 3.6 20.4 - - - +
137B ARG 2.9 17.1 + - - +
138B LEU* 3.7 14.2 - - - +
140B ARG* 1.3 76.9 - - - +
142B LYS* 1.3 83.2 + - - +
144B GLU* 3.4 1.6 + - - +
145B SER* 3.3 18.4 + - - -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 6.0 4.9 - - + -
237A GLN* 5.9 0.6 + - - -
506A PGE 4.5 24.0 - - - +
138B LEU* 3.2 21.5 + - + +
139B LEU* 3.2 8.8 + - + +
141B GLU* 1.3 98.2 + - - +
143B LEU* 1.3 62.8 + - + +
145B SER* 3.2 11.3 + - - +
146B LEU* 3.1 32.5 - - + +
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.6 9.6 - - + -
143A LEU* 3.9 26.0 - - + -
146A LEU* 4.5 17.9 - - + -
147A LEU* 5.9 2.9 - - + -
117B ILE* 3.2 34.3 - - + -
124B VAL* 3.8 22.0 - - + -
126B VAL* 4.2 15.7 - - + -
139B LEU* 2.8 26.6 + - + +
142B LYS* 1.3 79.8 - - + +
144B GLU* 1.3 61.9 + - - +
146B LEU* 3.3 5.0 + - + +
147B LEU* 3.1 34.2 + - + +
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 4.2 11.2 - - + -
240A GLN* 3.9 15.7 - - - +
258A LEU* 3.4 21.2 - - + +
261A ARG* 5.0 0.5 + - - -
116B ILE 3.8 0.3 - - - +
117B ILE* 3.2 25.3 - - + +
118B ASP 4.4 1.6 + - - -
119B ARG* 2.9 53.1 + - - +
140B ARG* 2.8 52.6 + - - +
141B GLU* 3.7 5.4 - - - +
142B LYS 3.4 0.2 - - - -
143B LEU* 1.3 78.4 - - - +
145B SER* 1.3 60.7 + - - +
147B LEU 3.3 6.9 - - - +
233B LEU* 5.0 4.0 - - - +
237B GLN* 4.2 2.4 + - - -
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 4.3 14.5 - - - +
236A LEU* 3.7 21.5 - - - +
141B GLU 3.3 5.6 + - - -
142B LYS* 3.2 15.9 + - - +
143B LEU 3.3 0.2 - - - -
144B GLU* 1.3 78.3 - - - +
146B LEU* 1.3 72.1 + - - +
233B LEU* 4.2 18.5 - - - +
236B LEU* 4.2 6.5 - - - +
237B GLN* 2.9 26.1 + - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.5 32.5 - - + -
505A PGE 3.7 26.2 - - - +
142B LYS* 3.1 22.4 - - + +
143B LEU* 3.3 8.4 + - + +
144B GLU 3.1 0.6 - - - -
145B SER* 1.3 86.6 - - - +
147B LEU* 1.3 61.9 + - + +
148B PRO* 3.2 12.1 - - - +
236B LEU* 3.6 16.4 - - + -
237B GLN* 4.3 5.3 - - + +
240B GLN* 3.0 32.1 - - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.3 27.8 - - + -
505A PGE 4.4 10.3 - - - +
117B ILE* 4.5 10.1 - - + +
119B ARG* 2.8 45.3 + - + +
122B LEU* 4.3 11.7 - - + -
124B VAL* 3.9 28.3 - - + -
143B LEU* 3.1 22.5 + - + +
144B GLU 3.3 3.3 + - - +
146B LEU* 1.3 84.8 - - + +
148B PRO* 1.3 68.7 - - + +
149B GLN 3.4 0.2 + - - -
151B LEU* 4.9 8.5 - - + -
237B GLN* 3.9 2.6 + - - -
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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