Contacts of the helix formed by residues 134 - 154 (chain B) in PDB entry 3SN5
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 GLN 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A SER* 3.6 2.5 + - - +
259A LEU* 3.5 40.5 + - + +
262A PHE* 3.5 41.3 - - + -
2134A UNX 3.6 12.5 - - - -
130B ILE 3.2 26.8 + - - +
131B LYS* 3.9 12.3 + - - +
133B LEU* 1.4 77.4 - - - +
135B GLY* 1.3 82.0 + - - +
137B ALA* 3.3 9.7 + - - +
138B LEU* 3.0 20.4 + - - -
448B LEU* 4.7 5.2 - - + -
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 3.4 21.1 + - - -
2134A UNX 3.3 16.8 - - - -
134B GLN* 1.3 79.5 + - - +
136B HIS* 1.4 60.5 + - - -
138B LEU* 3.2 5.7 + - - +
139B ASN* 3.0 32.4 + - - +
337B GLN* 3.8 2.4 + - - +
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.5 22.0 + - - -
253A ILE 5.0 10.5 - - - -
255A GLU* 3.4 46.8 + - + +
2134A UNX 3.6 4.4 - - - -
134B GLN 3.6 0.2 + - - -
135B GLY* 1.4 69.1 - - - -
137B ALA* 1.4 65.0 + - - +
139B ASN* 3.1 21.3 + - - +
140B SER* 3.2 16.9 + - - -
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS 3.8 7.2 - - - +
132B THR* 3.3 39.5 - - - +
134B GLN 3.3 5.2 + - - +
136B HIS* 1.4 76.2 - - - +
138B LEU* 1.3 57.3 + - - +
140B SER* 3.5 7.4 + - - -
141B LEU* 3.1 27.7 + - - +
255B GLU* 4.1 23.3 - - + +
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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
----------------------------------------------------------
132B THR 4.2 1.3 + - - -
133B LEU 3.7 16.4 - - - +
134B GLN* 3.0 23.3 + - - +
135B GLY 3.5 9.2 - - - +
137B ALA* 1.3 74.5 - - - +
139B ASN* 1.4 56.7 + - - +
141B LEU* 4.1 11.0 - - + -
142B THR* 2.7 49.5 + - - +
337B GLN* 3.4 24.5 - - - +
448B LEU* 3.7 32.5 - - + -
449B PHE* 3.7 33.2 - - + -
452B HIS* 4.2 2.2 - - + +
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLY 3.0 20.8 + - - +
136B HIS* 3.1 16.0 + - - +
138B LEU* 1.4 75.8 - - - +
140B SER* 1.3 59.0 + - - +
142B THR* 3.2 4.0 + - - -
143B GLU* 2.9 29.5 + - - +
336B SER* 6.2 0.6 - - - +
337B GLN* 2.7 38.9 + - - +
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B HIS 3.2 12.9 + - - -
137B ALA* 3.5 9.7 + - - -
139B ASN* 1.3 78.5 - - - +
141B LEU* 1.4 51.6 + - - +
143B GLU* 3.6 7.4 - - - +
144B SER* 2.8 36.8 + - - -
255B GLU* 5.2 7.1 - - - +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B THR 4.5 6.5 - - - +
133B LEU* 3.6 30.5 - - + -
137B ALA 3.1 19.0 + - - +
138B LEU* 3.6 10.3 - - + +
140B SER* 1.4 73.2 - - - +
142B THR* 1.4 56.6 + - - +
144B SER* 4.5 1.1 - - - -
145B MET 3.1 21.8 + - - -
186B THR* 3.2 30.4 - - + +
187B ILE* 3.9 14.1 - - + -
254B SER* 3.7 30.7 - - - -
255B GLU 5.6 0.2 - - - +
256B LEU* 5.9 1.6 - - + -
449B PHE* 3.6 34.9 - - + -
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 2.7 28.3 + - - +
139B ASN* 3.5 5.6 - - - -
141B LEU* 1.4 72.9 - - - +
143B GLU* 1.3 64.5 + - - +
145B MET* 3.4 3.0 + - - +
146B MET 3.3 9.4 + - - -
335B LEU 5.2 5.8 - - - +
337B GLN* 4.4 9.1 - - + +
340B LEU* 3.7 13.5 - - + -
449B PHE* 4.4 8.2 - - - -
452B HIS* 3.1 37.6 + - + +
456B GLN* 3.0 37.9 + - - +
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN 2.9 20.2 + - - +
140B SER* 3.6 8.7 - - - +
142B THR* 1.3 71.3 - - - +
144B SER* 1.3 61.4 + - - +
146B MET* 3.5 7.9 + - - +
147B GLU* 3.3 27.8 + - + +
334B CYS* 5.5 11.4 - - - -
335B LEU 5.9 3.1 - - - +
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER 2.8 18.9 + - - -
141B LEU* 3.7 5.8 - - - -
143B GLU* 1.3 73.7 - - - +
145B MET* 1.4 58.7 + - - +
147B GLU* 3.2 7.8 + - - +
148B ASN* 2.9 50.0 + - - -
185B LEU 4.8 1.0 + - - -
186B THR* 3.8 15.5 + - - +
190B ARG* 4.1 11.7 + - - +
252B SER* 4.9 7.2 + - - -
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU 3.1 18.4 + - - +
142B THR 3.4 2.2 + - - +
144B SER* 1.4 74.0 - - - +
146B MET* 1.4 52.9 + - - +
149B LEU* 2.8 47.3 + - + +
179B MET* 4.0 16.6 - - + +
182B ALA* 3.6 29.4 - - + -
183B GLY* 3.9 10.1 - - - +
186B THR* 3.3 23.0 - - - +
449B PHE* 3.9 13.0 - - + -
453B GLU* 3.4 38.1 - - + +
456B GLN* 3.4 19.5 - - - +
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Residues in contact with MET 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B THR 3.3 4.1 + - - +
143B GLU* 3.7 10.1 - - - +
144B SER 3.3 0.2 - - - -
145B MET* 1.4 78.2 - - - +
147B GLU* 1.4 61.1 + - + +
149B LEU* 3.6 2.5 + - - +
150B GLN* 3.2 49.8 + - - +
333B ILE* 3.5 32.5 - - + +
334B CYS* 5.0 0.9 - - - -
335B LEU* 3.8 32.3 - - + +
456B GLN* 3.4 48.2 + - + +
459B ILE* 4.9 2.5 - - + -
460B LEU* 3.9 22.9 - - + -
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU* 3.3 16.2 + - + +
144B SER* 3.2 11.1 + - - +
146B MET* 1.4 75.2 - - + +
148B ASN* 1.4 59.7 + - - +
150B GLN* 3.5 7.7 + - - +
151B ARG* 3.0 54.4 + - - +
190B ARG* 5.1 2.2 - - - +
332B PRO* 5.5 12.8 - - + -
334B CYS* 6.2 4.0 - - - -
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Residues in contact with ASN 148 (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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144B SER* 2.9 32.3 + - - +
145B MET 3.8 2.9 - - - +
147B GLU* 1.4 71.6 - - - +
149B LEU* 1.4 66.0 + - - +
151B ARG* 2.9 29.5 + - - +
152B ILE* 3.1 31.6 + - + +
182B ALA* 4.0 13.9 - - - +
185B LEU* 3.7 20.0 + - + +
186B THR* 2.8 35.1 + - - +
190B ARG* 3.3 15.3 + - - +
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Residues in contact with LEU 149 (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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145B MET* 2.8 39.7 + - + +
146B MET* 4.0 1.3 - - - +
148B ASN* 1.4 69.9 - - - +
150B GLN* 1.3 52.6 + - - +
152B ILE* 3.2 4.4 + - - +
153B MET* 2.8 46.1 + - - +
178B VAL* 3.7 28.5 - - + -
179B MET* 4.1 14.8 - - - -
182B ALA* 3.8 19.9 - - + +
453B GLU 4.2 3.4 - - - +
456B GLN* 3.8 29.6 - - + -
457B PHE* 4.0 13.2 - - + +
460B LEU* 3.6 16.2 - - + -
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Residues in contact with GLN 150 (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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146B MET* 3.2 30.6 + - - +
147B GLU* 3.8 5.2 - - - +
148B ASN 3.4 0.2 - - - -
149B LEU* 1.3 72.2 - - - +
151B ARG* 1.4 63.7 + - - +
153B MET 4.5 0.2 - - - +
154B ARG* 3.1 39.9 + - - +
332B PRO* 3.3 20.5 - - + +
333B ILE* 2.9 57.9 + - - +
460B LEU* 3.7 16.8 - - + -
464B TYR* 3.2 28.1 + - - +
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Residues in contact with ARG 151 (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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147B GLU* 3.0 27.5 + - - +
148B ASN* 2.9 50.7 + - - +
150B GLN* 1.4 75.3 - - - +
152B ILE* 1.3 64.1 + - + +
154B ARG* 3.9 13.8 - - - +
185B LEU* 6.2 3.4 - - + -
190B ARG* 3.6 39.3 - - - +
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Residues in contact with ILE 152 (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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148B ASN 3.1 17.8 + - - +
149B LEU* 3.6 5.6 - - - +
151B ARG* 1.3 79.7 - - + +
153B MET* 1.3 61.1 + - - +
154B ARG 3.5 5.4 + - - +
177B ARG* 5.0 8.3 + - - +
178B VAL* 4.3 31.4 - - + +
181B GLU* 3.6 37.5 - - + +
182B ALA* 3.4 38.1 - - + +
185B LEU* 4.2 9.2 - - + -
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 2.8 33.2 + - - +
152B ILE* 1.3 70.3 - - - +
154B ARG* 1.4 61.3 + - - +
174B PHE* 5.3 2.9 - - + -
178B VAL* 3.7 35.7 - - + -
457B PHE* 4.1 7.9 - - + +
460B LEU* 3.7 34.3 - - + -
461B MET* 3.6 39.5 - - + +
464B TYR* 4.0 17.4 - - + -
465B PHE* 3.7 28.9 - - + -
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 3.1 26.1 + - - +
151B ARG* 3.9 13.0 - - - +
152B ILE 3.4 5.0 - - - +
153B MET* 1.4 80.4 - - - +
327B SER 2.8 24.9 + - - +
328B LEU* 3.1 36.1 + - + +
330B GLY 3.3 19.2 + - - -
331B ASN 3.2 25.2 + - - -
332B PRO* 4.0 21.5 - - - +
333B ILE* 6.0 1.2 - - - +
464B TYR* 3.3 30.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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