Contacts of the helix formed by residues 135 - 148 (chain B) in PDB entry 6FEQ
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 THR 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B LEU* 1.3 79.1 - - - +
136B VAL* 1.3 63.9 + - - +
137B ARG* 3.6 10.5 - - + +
138B GLU* 3.2 37.9 + - + +
139B ASN* 3.0 32.9 + - - -
174B ALA 3.8 0.3 + - - -
175B ASP* 3.1 13.2 - - + +
176B SER 2.5 40.7 + - - -
177B LYS* 4.5 2.5 - - - -
178B VAL* 4.1 0.4 - - - -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B THR* 1.3 76.8 + - - +
137B ARG* 1.3 63.4 + - - +
139B ASN* 3.9 7.3 - - - +
140B LEU* 3.2 39.5 + - + +
165B ILE* 4.2 14.8 - - + -
170B LEU* 4.5 13.0 - - + -
173B VAL* 4.1 23.6 - - + +
174B ALA 4.5 1.8 - - - +
176B SER 4.5 3.1 - - - +
178B VAL* 4.0 16.6 - - + -
186B VAL* 5.2 7.9 - - + -
194B THR* 3.5 36.6 - - + +
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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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135B THR* 3.2 6.7 - - + -
136B VAL* 1.3 79.8 - - - +
138B GLU* 1.3 62.8 + - + +
140B LEU* 4.2 2.7 - - - +
141B GLN* 3.3 49.0 + - - +
158B ASN* 4.8 3.1 + - - +
161B ILE* 3.5 27.3 - - - +
162B ASN* 3.2 29.1 + - - +
165B ILE* 4.1 24.1 - - - +
174B ALA* 3.4 23.9 + - - +
175B ASP* 3.3 26.8 + - - +
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Residues in contact with GLU 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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134B LEU* 3.4 37.7 - - + +
135B THR* 3.2 23.3 + - + +
137B ARG* 1.3 77.6 - - + +
139B ASN* 1.3 64.8 - - - +
141B GLN* 3.5 14.4 + - - +
142B PHE* 3.1 21.0 + - - +
386B LYS* 3.9 30.2 + - + +
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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
----------------------------------------------------------
130B VAL* 4.6 3.9 - - - +
131B MET* 3.3 50.3 + - - +
134B LEU* 3.6 10.0 - - - +
135B THR 3.0 22.4 + - - +
136B VAL* 3.9 7.1 - - - +
137B ARG 3.3 0.4 - - - -
138B GLU* 1.3 76.4 - - - +
140B LEU* 1.3 63.6 + - + +
142B PHE* 2.9 23.3 + - - +
143B SER* 3.0 14.2 + - - -
178B VAL* 3.7 14.6 - - - +
194B THR* 4.6 12.2 - - + +
198B MET* 5.0 14.0 - - + +
383B ARG* 5.5 0.7 - - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.2 33.8 + - + +
137B ARG 4.4 0.2 - - - +
139B ASN* 1.3 73.2 - - + +
141B GLN* 1.3 61.2 + - - +
143B SER* 3.9 3.7 - - - +
144B ALA* 3.1 27.0 + - - +
161B ILE* 3.8 31.7 - - + +
164B VAL* 4.6 17.0 - - + -
165B ILE* 4.8 10.8 - - + -
168B LEU* 5.6 3.4 - - + -
170B LEU* 6.3 0.4 - - + -
194B THR* 4.3 7.0 - - + +
197B GLY* 3.8 8.1 - - - +
198B MET* 3.8 44.2 - - + +
201B ILE* 4.2 9.9 - - + +
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Residues in contact with GLN 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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137B ARG* 3.3 39.8 + - - +
138B GLU* 3.8 13.4 - - - +
139B ASN 3.2 0.8 - - - -
140B LEU* 1.3 75.9 - - - +
142B PHE* 1.3 59.0 + - - +
144B ALA* 3.8 2.6 - - - +
145B ALA* 2.9 31.5 + - - +
154B ASN* 5.5 1.5 + - - -
158B ASN* 3.3 21.0 + - - +
161B ILE* 3.7 19.7 - - + -
379B TRP* 5.1 15.6 - - + -
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Residues in contact with PHE 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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131B MET* 6.0 0.2 - - + -
134B LEU* 5.9 1.6 - - + -
138B GLU 3.1 13.1 + - - +
139B ASN* 2.9 14.3 + - - +
141B GLN* 1.3 77.1 - - - +
143B SER* 1.3 65.1 + - - +
145B ALA* 3.4 10.9 + - - +
146B LEU* 3.6 43.3 + - + +
198B MET* 5.6 7.0 - - + -
379B TRP* 3.4 41.5 - + + -
380B VAL* 4.4 7.6 - - + -
383B ARG* 3.2 46.7 - - + -
458B GLU* 3.9 19.7 - - - -
463B TYR* 4.5 9.0 - + - -
464B TYR* 5.0 4.7 - + - -
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Residues in contact with SER 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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139B ASN 3.0 13.7 + - - -
140B LEU* 4.1 3.6 - - - -
141B GLN 3.3 0.2 - - - -
142B PHE* 1.3 81.3 - - - +
144B ALA* 1.3 61.4 + - - +
146B LEU* 4.2 1.0 - - - +
147B ARG* 3.3 38.1 + - - +
198B MET* 2.9 43.4 + - - -
201B ILE* 3.4 14.7 - - - +
463B TYR* 4.1 9.3 + - - -
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Residues in contact with ALA 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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140B LEU 3.1 19.7 + - - +
141B GLN* 3.8 4.7 - - - +
143B SER* 1.3 76.1 - - - +
145B ALA* 1.3 62.5 + - - +
146B LEU 3.2 1.0 + - - -
148B LEU* 3.4 34.0 + - + +
157B LYS* 4.0 18.7 + - + +
161B ILE* 4.3 15.0 - - + -
201B ILE* 3.7 22.8 - - + +
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Residues in contact with ALA 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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141B GLN 2.9 18.0 + - - +
142B PHE* 3.4 5.1 + - - +
143B SER 3.3 0.6 - - - -
144B ALA* 1.3 77.7 - - - +
146B LEU* 1.3 66.0 + - + +
148B LEU 4.5 6.0 - - - +
157B LYS* 4.4 13.2 + - + +
371B THR* 4.6 2.9 - - - +
375B HIS* 3.6 18.1 + - - +
379B TRP* 4.0 40.6 - - + +
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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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142B PHE* 3.6 47.8 + - + +
143B SER 3.6 1.7 + - - +
144B ALA 3.2 0.6 - - - -
145B ALA* 1.3 89.6 - - + +
147B ARG* 1.3 61.9 + - - +
148B LEU 4.5 0.2 - - - -
370B THR* 4.7 5.0 - - - +
371B THR* 3.8 17.9 + - + -
375B HIS* 4.7 4.9 - - + -
376B GLN* 4.1 28.5 - - + -
379B TRP* 4.6 10.5 - - + -
380B VAL* 4.7 4.7 - - + -
462B GLY 4.6 3.3 - - - +
463B TYR* 3.6 51.6 - - + +
464B TYR* 4.2 7.6 - - + -
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Residues in contact with ARG 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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118B LYS 5.5 0.8 + - - -
119B CYS* 3.8 16.4 + - - +
121B SER 3.9 10.3 + - - -
143B SER* 3.3 24.5 + - - +
146B LEU* 1.3 83.4 - - - +
148B LEU* 1.3 70.8 + - + +
198B MET 3.1 23.6 + - - -
199B GLU* 3.5 33.0 + - - +
201B ILE* 4.4 9.8 - - + +
202B THR* 3.7 32.6 - - - +
370B THR* 3.6 17.5 - - - +
461B SER* 5.6 4.3 + - - +
462B GLY 5.9 0.2 - - - +
463B TYR* 3.5 34.2 + - + -
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Residues in contact with LEU 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 ALA* 3.4 24.8 + - + +
145B ALA 4.5 3.8 - - - +
146B LEU 4.5 2.3 - - - -
147B ARG* 1.3 83.4 + - + +
149B ALA* 1.3 66.8 + - - +
150B THR* 5.4 0.9 - - - +
152B MET* 3.9 34.1 - - + -
157B LYS* 4.0 14.6 + - + -
160B ARG* 4.7 19.3 - - + +
201B ILE* 4.2 27.6 - - + +
202B THR* 4.3 26.0 - - - +
370B THR* 5.0 0.2 - - - -
371B THR* 4.5 6.2 + - - +
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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