Contacts of the helix formed by residues 132 - 144 (chain B) in PDB entry 5H1C
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 GLY 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG 3.4 1.6 - - - -
131B THR* 1.3 73.8 - - - +
133B LYS* 1.3 57.8 + - - +
134B THR 3.4 1.8 - - - -
135B GLN* 3.1 12.8 - - - +
136B ILE* 3.0 32.9 + - - +
310B ARG* 3.4 0.8 - - - +
327B PHE* 5.5 0.3 - - - -
329B ILE* 3.9 16.0 - - - +
602B ANP 2.5 31.1 + - - -
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 3.8 19.5 - - + +
127B GLY* 5.0 8.5 - - - -
128B GLU 5.0 0.8 - - - -
129B PHE* 4.2 13.7 - - - +
131B THR* 3.3 19.3 + - - +
132B GLY* 1.3 74.9 - - - +
134B THR* 1.3 66.2 + - + +
136B ILE* 3.2 8.0 + - - +
137B CYS* 3.0 31.2 + - - -
222B ASP* 5.2 2.0 - - - -
266B THR* 3.3 30.7 - - + -
267B ASN 4.7 13.2 - - - +
268B GLN* 4.3 16.2 + - - +
302B LEU* 4.2 12.3 - - + -
601B MG 4.4 2.2 - - - -
602B ANP 2.4 51.3 + - - +
294C HIS* 4.7 3.9 + - - -
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Residues in contact with THR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LYS* 1.3 78.2 - - + +
135B GLN* 1.3 61.1 + - - +
137B CYS* 3.1 11.5 + - - +
138B HIS* 2.9 41.9 + - - -
159B TYR* 4.9 5.5 + - - -
165B THR* 4.6 6.2 + - - +
222B ASP* 2.1 30.5 - - + +
266B THR* 5.0 0.4 - - + -
601B MG 1.6 37.0 - - - -
602B ANP 2.9 20.4 + - - +
318C PRO* 5.1 8.0 - - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLY* 3.1 22.4 - - - +
134B THR* 1.3 81.1 + - - +
136B ILE* 1.3 58.4 + - - +
138B HIS* 2.9 27.8 + - - +
139B THR* 3.0 16.3 + - + +
170B ARG* 2.6 52.7 + - - +
329B ILE* 3.7 25.2 - - + +
333B GLY* 4.4 10.4 - - - -
334B VAL* 4.8 6.5 - - + -
602B ANP 3.4 29.5 + - - +
318C PRO* 4.7 2.8 + - - +
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Residues in contact with ILE 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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104B THR* 5.8 7.2 - - + +
109B LEU* 5.0 9.4 - - + -
117B ILE* 5.8 0.7 - - + -
125B MET* 4.0 19.1 - - + -
132B GLY 3.0 16.0 + - - +
133B LYS* 3.2 6.9 + - - +
135B GLN* 1.3 78.7 - - - +
137B CYS* 1.3 63.1 + - - +
139B THR* 2.9 23.2 + - - +
140B LEU* 2.9 32.8 + - + +
300B LEU* 6.6 0.2 - - + -
302B LEU* 4.2 20.2 - - + -
327B PHE* 3.8 26.0 - - + -
334B VAL* 3.7 20.4 - - + -
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Residues in contact with CYS 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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125B MET* 5.1 4.3 - - - -
133B LYS 3.0 20.5 + - - -
134B THR* 3.1 16.1 + - + +
136B ILE* 1.3 78.0 - - - +
138B HIS* 1.3 61.7 + - - +
140B LEU* 3.9 4.9 - - - +
141B ALA* 3.0 24.0 + - - +
159B TYR* 4.2 11.2 - - + +
220B ILE* 3.3 38.5 - - + +
222B ASP* 5.1 3.4 - - - -
264B VAL* 4.5 13.2 - - - -
266B THR* 3.9 20.2 - - - -
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Residues in contact with HIS 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 THR* 2.9 35.2 + - - -
135B GLN* 2.9 18.8 + - - +
137B CYS* 1.3 77.5 - - - +
139B THR* 1.3 60.1 + - + +
141B ALA* 2.8 23.7 + - - +
142B VAL* 3.0 11.1 + - - +
159B TYR* 4.3 9.2 + - - -
165B THR 4.5 4.2 + - - -
166B PHE* 3.7 22.7 - + - -
167B ARG* 3.3 40.5 + - - +
170B ARG* 4.2 20.2 - - + -
171B LEU* 3.8 26.9 - - + +
174B VAL* 5.2 1.3 - - + -
318C PRO* 5.5 5.5 - - + +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR 3.9 16.5 + - - -
105B GLY* 5.9 1.1 - - - -
135B GLN* 3.0 16.7 + - - +
136B ILE* 2.9 20.8 + - - +
138B HIS* 1.3 76.9 - - + +
140B LEU* 1.3 58.2 + - - +
142B VAL* 3.4 1.6 + - - +
143B THR* 2.8 38.0 + - - +
174B VAL* 4.0 27.8 - - + -
177B ARG* 5.5 2.9 - - - +
178B TYR* 6.0 0.9 - - - -
332B ASP 4.3 11.4 - - - +
333B GLY* 5.1 0.4 - - - -
334B VAL* 4.0 23.1 - - + +
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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
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102B ILE* 5.0 7.9 - - + +
103B THR 3.9 8.5 - - - +
104B THR* 3.8 36.6 - - + +
117B ILE* 3.6 29.2 - - + -
125B MET* 5.2 0.4 - - + -
136B ILE* 2.9 36.3 + - + +
137B CYS* 3.9 7.4 - - - +
139B THR* 1.3 78.4 + - - +
141B ALA* 1.3 64.3 + - - +
143B THR* 3.2 3.3 + - - +
144B CYS* 3.0 31.9 + - - -
218B LEU* 4.0 14.4 - - + -
220B ILE* 4.8 0.2 - - + -
264B VAL* 4.7 18.2 - - + -
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Residues in contact with ALA 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 CYS 3.0 15.8 + - - +
138B HIS* 2.8 15.7 + - - +
140B LEU* 1.3 79.3 - - - +
142B VAL* 1.3 58.6 + - - +
144B CYS* 4.3 4.0 + - - +
145B GLN* 4.6 5.0 - - - +
157B ALA* 3.9 25.7 - - + +
159B TYR* 5.0 8.5 - - + -
166B PHE* 5.9 1.3 - - + -
171B LEU* 4.6 8.5 - - + -
189B VAL* 4.5 18.9 - - + +
218B LEU* 4.9 1.1 - - - -
220B ILE* 3.9 16.2 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B HIS 3.0 5.0 + - - +
139B THR 4.0 1.3 - - - +
141B ALA* 1.3 75.9 - - - +
143B THR* 1.3 60.8 + - - +
144B CYS 3.2 2.7 - - - -
145B GLN* 3.0 28.5 + - - +
146B LEU* 4.3 2.5 + - + +
171B LEU* 3.5 39.3 - - + +
174B VAL* 3.6 37.7 - - + +
175B ALA* 4.7 1.6 - - - +
178B TYR* 4.9 6.5 - - + -
180B LEU* 5.8 4.4 - - + +
185B VAL* 3.8 37.2 - - + -
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Residues in contact with THR 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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102B ILE* 4.4 4.6 - - - +
103B THR* 3.8 21.5 + - - +
104B THR 4.9 0.7 - - - -
105B GLY* 4.7 10.5 - - - -
139B THR* 2.8 27.0 + - - +
140B LEU* 3.2 14.7 + - - +
142B VAL* 1.3 72.2 - - - +
144B CYS* 1.3 65.2 + - - +
145B GLN 3.0 1.9 + - - -
146B LEU* 3.5 26.4 + - + +
152B GLY* 3.5 12.3 + - - -
174B VAL* 4.7 1.8 - - + -
178B TYR* 3.4 38.8 - - + +
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Residues in contact with CYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.6 29.8 - - + -
140B LEU* 3.0 21.9 + - - +
141B ALA* 4.5 7.2 - - - +
142B VAL 3.2 0.6 + - - -
143B THR* 1.3 79.4 - - - +
145B GLN* 1.3 59.0 + - + +
146B LEU 3.3 0.2 - - - -
152B GLY* 3.4 5.1 - - - -
153B GLY 3.0 22.6 + - - +
154B GLU* 3.0 10.6 + - - -
155B GLY 3.9 6.8 + - - +
157B ALA* 5.0 2.7 - - + -
217B ALA* 3.6 17.7 - - + -
218B LEU* 3.7 31.4 - - + -
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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