Contacts of the helix formed by residues 148 - 163 (chain B) in PDB entry 5ANC
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 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.0 16.0 - - - +
35B SER 5.2 5.6 + - - -
78B MET* 5.3 9.4 - - - +
129B GLY 5.2 1.8 + - - -
146B GLY 5.1 0.2 - - - -
147B ASN* 1.3 74.6 - - - +
149B LEU* 1.3 68.7 + - - +
150B GLU* 3.9 15.8 + - - -
151B LEU* 3.1 42.7 + - - +
152B LEU* 3.2 14.8 + - - +
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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
----------------------------------------------------------
77B ASN* 3.5 34.4 + - + +
78B MET* 6.0 1.0 - - - +
86B TYR* 3.3 50.6 - - + +
88B TYR* 4.0 14.1 - - + +
147B ASN 3.2 8.1 + - - -
148B SER* 1.3 71.6 + - - +
150B GLU* 1.3 63.2 + - + +
151B LEU 3.0 2.1 + - - -
152B LEU* 3.9 1.4 - - - +
153B SER* 2.5 44.2 + - - +
183B ASN* 4.4 12.3 - - - +
3447N U 3.3 33.0 - - - +
3448N G 3.8 3.4 - - - +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LYS* 3.5 31.1 + - - +
74B ILE* 3.3 39.2 - - - +
77B ASN* 5.9 2.9 - - + +
78B MET* 4.4 9.9 - - - +
148B SER* 3.2 13.4 + - - +
149B LEU* 1.3 83.6 - - + +
151B LEU* 1.3 65.0 + - + +
153B SER 4.4 0.4 - - - -
154B GLN* 3.5 22.7 + - - +
3446N C 3.6 10.2 + - - +
3447N U 3.3 37.1 + - + +
3460N G 6.0 0.8 + - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER 5.9 2.7 - - - +
36B LYS* 6.5 0.7 - - + -
127B LEU* 4.0 28.8 - - + +
128B ASP 4.9 11.9 - - - +
130B ILE* 4.4 3.4 - - + -
148B SER* 3.1 33.5 + - - +
150B GLU* 1.3 84.4 - - + +
152B LEU* 1.3 62.9 + - - +
153B SER 3.2 0.7 - - - -
154B GLN* 3.2 14.5 - - - +
155B SER* 2.9 33.1 + - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR* 3.3 37.7 - - + +
88B TYR* 3.4 28.5 - - + -
129B GLY 5.4 0.2 - - - +
130B ILE* 3.5 42.0 - - + +
144B LEU* 3.4 29.4 - - + +
145B THR 3.9 3.6 - - - -
146B GLY* 3.8 8.5 - - - +
148B SER 3.2 12.3 + - - +
149B LEU 3.9 1.1 - - - +
151B LEU* 1.3 78.1 - - - +
153B SER* 1.3 57.7 + - - +
155B SER* 3.2 4.0 + - - -
156B CYS* 2.9 35.0 + - - -
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Residues in contact with SER 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 2.7 49.1 + - - -
149B LEU* 2.5 27.8 + - - +
152B LEU* 1.3 78.3 - - - +
154B GLN* 1.3 55.5 + - - +
156B CYS* 3.2 3.8 + - - +
157B ALA* 2.9 28.9 + - - +
3446N C 3.7 26.1 - - - +
3447N U 4.2 2.7 - - - -
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.7 21.8 - - + +
150B GLU 3.5 17.0 + - - +
151B LEU* 3.2 17.7 + - - +
153B SER* 1.3 79.7 - - - +
155B SER* 1.3 53.5 + - - +
157B ALA* 3.2 9.3 + - - +
158B THR* 2.7 36.2 + - - -
3445N G 3.6 15.7 - - - +
3446N C 3.7 16.3 + - - +
3460N G 5.1 1.4 - - - +
3461N U 3.4 13.6 + - - -
3462N C 2.8 48.4 + - - +
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 5.5 0.3 - - - +
125B GLU 5.2 0.8 + - - -
126B LEU* 3.9 18.2 - - - +
127B LEU* 3.4 18.7 + - - +
130B ILE* 3.1 29.2 - - - +
151B LEU 2.9 11.6 + - - -
152B LEU 3.4 9.2 - - - -
154B GLN* 1.3 75.5 - - - +
156B CYS* 1.3 64.2 + - - +
158B THR* 3.2 10.1 + - - -
159B ILE* 3.0 29.1 + - - +
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Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 3.5 43.1 - - + -
90B MET* 3.1 22.0 - - + +
144B LEU* 4.1 18.6 - - - -
152B LEU* 2.9 33.9 + - - -
153B SER 3.4 7.4 - - - +
155B SER* 1.3 75.7 - - - +
157B ALA* 1.3 57.7 + - - +
159B ILE* 3.2 10.3 + - - +
160B GLN* 2.9 24.6 + - - +
179B VAL* 4.5 5.2 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER 2.9 12.6 + - - +
154B GLN* 3.3 9.6 - - - +
156B CYS* 1.3 77.5 - - - +
158B THR* 1.3 57.2 + - - +
160B GLN* 3.2 14.1 + - - +
161B LEU* 2.9 32.0 + - - +
3445N G 3.2 28.9 + - - +
3446N C 3.7 18.6 - - - +
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Residues in contact with THR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.7 31.4 - - + -
154B GLN 2.7 23.6 + - - -
155B SER* 3.2 10.4 + - - -
157B ALA* 1.3 75.3 - - - +
159B ILE* 1.3 58.6 + - - +
161B LEU* 3.2 12.7 + - + +
162B ARG* 2.9 40.1 + - + +
3462N C 4.0 14.1 + - - +
3463N A 5.0 20.6 - - - +
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 4.1 10.3 - - + -
110B VAL* 4.5 16.8 - - + -
112B ILE* 5.1 3.5 - - + +
124B ILE* 4.0 23.3 - - + +
126B LEU* 3.6 13.2 - - + -
142B ILE* 6.1 2.2 - - + -
144B LEU* 3.6 36.6 - - + -
155B SER 3.0 20.2 + - - +
156B CYS* 3.3 13.7 - - - +
158B THR* 1.3 75.9 - - - +
160B GLN* 1.3 64.6 + - - +
162B ARG* 3.2 9.1 + - - +
163B SER 3.0 18.0 + - - -
177B ILE* 3.3 29.4 - - + +
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Residues in contact with GLN 160 (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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90B MET* 4.1 7.0 - - + -
156B CYS 2.9 11.9 + - - +
157B ALA* 3.3 16.0 - - - +
159B ILE* 1.3 76.7 - - - +
161B LEU* 1.3 61.6 + - - +
163B SER* 3.0 24.3 + - - +
164B ALA* 4.2 2.1 - - - +
177B ILE* 3.0 29.3 - - - +
178B TYR* 3.8 9.7 - - + -
179B VAL* 3.4 25.3 - - - +
182B ARG* 4.4 9.0 + - - -
12H TYR* 3.2 42.5 - - - +
3446N C 5.4 1.2 + - - -
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Residues in contact with LEU 161 (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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122B ARG* 4.9 1.7 + - - -
157B ALA 2.9 13.4 + - - +
158B THR* 3.4 14.8 - - + +
160B GLN* 1.3 74.8 - - - +
162B ARG* 1.3 66.6 + - + +
164B ALA* 3.1 25.8 + - + +
166B LYS* 5.4 14.7 + - - +
25H ARG* 5.8 0.2 - - - +
3444N G 3.4 57.0 - - + +
3445N G 5.1 7.4 - - - +
3463N A 4.4 19.5 - - - +
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Residues in contact with ARG 162 (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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112B ILE* 4.7 10.5 - - + -
115B PHE* 3.9 1.6 - - - -
122B ARG* 2.9 69.3 + - - +
123B ARG 3.0 27.0 + - - +
124B ILE* 3.7 32.2 - - + +
158B THR* 2.9 23.8 + - + +
159B ILE* 3.2 11.2 + - - +
161B LEU* 1.3 77.2 - - - +
163B SER* 1.3 55.8 + - - +
164B ALA 2.9 7.6 + - - +
3463N A 4.9 10.0 + - - -
3464N G 4.4 15.3 + - - -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 3.8 9.9 - - - +
112B ILE* 3.9 15.8 - - - +
115B PHE* 3.3 16.1 - - - -
159B ILE 3.0 6.9 + - - -
160B GLN 3.0 12.9 + - - +
162B ARG* 1.3 69.9 - - - +
164B ALA* 1.3 59.9 + - - +
175B ASP 4.3 1.4 - - - +
176B GLY* 3.5 19.3 - - - -
177B ILE* 3.1 50.1 + - - +
178B TYR* 5.1 2.8 + - - -
13H LYS* 5.5 1.0 + - - -
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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