Contacts of the helix formed by residues 155 - 165 (chain B) in PDB entry 1CCW
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 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B HIS* 3.2 21.8 + - - -
152B THR* 3.7 14.6 - - - -
153B PRO 3.8 2.2 + - - -
154B ASP* 1.3 73.9 - - - +
156B ARG* 1.3 58.8 + - - +
157B LEU 3.4 2.2 - - - -
158B LEU* 3.4 14.6 + - - +
159B ALA* 2.8 26.5 + - - +
170B ASN* 4.2 5.9 + - - -
193B ASP* 5.1 1.0 - - - +
194B TRP* 3.5 29.9 - - - +
197B CYS* 3.7 9.6 - - - -
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Residues in contact with ARG 156 (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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8B TRP* 5.9 0.7 - - - -
16B GLN* 4.2 15.6 + - - -
19B GLU* 5.2 4.0 + - - +
20B VAL* 3.6 31.4 - - + +
23B GLN* 3.3 18.3 + - - +
154B ASP* 2.8 38.5 + - - +
155B SER* 1.3 76.8 - - - +
157B LEU* 1.3 65.3 + - - +
159B ALA* 3.3 2.8 + - - +
160B GLU* 3.0 24.8 + - - +
189B LYS* 3.9 14.5 - - - +
193B ASP* 3.4 38.2 + - + +
196B TYR* 3.5 43.1 - - + -
197B CYS* 3.9 3.3 - - - -
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Residues in contact with LEU 157 (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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20B VAL* 3.5 24.7 - - + +
21B LEU* 4.2 20.9 - - + -
23B GLN* 3.9 20.6 - - + +
24B TRP* 3.8 27.6 - - + +
27B GLY* 4.2 9.2 - - - -
104B TYR* 4.1 12.6 - - + +
128B VAL* 3.7 25.1 - - + -
154B ASP* 5.0 1.2 + - - -
155B SER 3.4 0.2 - - - -
156B ARG* 1.3 75.8 - - - +
158B LEU* 1.3 67.5 + - - +
160B GLU* 3.2 1.9 + - + +
161B ILE* 3.0 41.2 + - + +
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Residues in contact with LEU 158 (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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95B ILE* 4.3 25.8 - - + -
99B THR* 4.5 9.6 - - + -
104B TYR* 5.1 2.1 + - - +
127B GLY* 4.5 0.9 - - - -
128B VAL* 3.8 34.7 - - + +
148B ALA* 5.3 1.6 - - + -
150B HIS* 3.6 43.3 - - + +
152B THR* 4.3 8.7 - - + +
155B SER* 3.7 13.8 - - - +
156B ARG 3.4 0.2 - - - -
157B LEU* 1.3 78.4 - - - +
159B ALA* 1.3 58.2 + - - +
161B ILE* 3.3 2.3 + - + +
162B ILE* 2.9 55.5 + - + +
170B ASN* 5.7 0.7 - - - +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B SER* 2.8 17.6 + - - +
156B ARG 3.5 5.4 - - - +
158B LEU* 1.3 73.1 - - - +
160B GLU* 1.3 67.4 + - - +
162B ILE* 4.0 8.3 - - - -
163B HIS* 3.0 35.3 + - + +
170B ASN* 4.0 20.4 - - - +
196B TYR* 5.4 0.2 - - + -
197B CYS* 4.1 15.7 - - + -
200B LEU* 3.8 13.7 - - + -
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Residues in contact with GLU 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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17B ARG* 2.8 42.2 + - - -
20B VAL* 4.6 0.4 - - + -
21B LEU* 4.0 21.8 - - + -
30B VAL* 3.5 13.5 - - + +
32B LEU* 4.1 2.3 - - - +
156B ARG 3.0 17.0 + - - +
157B LEU* 3.2 9.8 + - + +
159B ALA* 1.3 77.6 - - - +
161B ILE* 1.3 57.9 + - - +
163B HIS* 4.4 0.7 - - - +
164B ALA* 3.0 31.5 + - - +
196B TYR* 2.4 36.1 + - + +
200B LEU* 3.8 22.7 - - + +
204B TYR* 5.0 1.6 + - - -
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Residues in contact with ILE 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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26B THR* 3.4 30.5 - - - +
30B VAL* 4.2 15.3 - - + -
127B GLY 3.7 13.9 - - - +
128B VAL* 3.7 26.0 - - + +
131B GLY 3.5 30.1 - - - +
132B VAL* 3.6 11.3 - - + +
135B CYS* 4.1 5.3 - - - +
157B LEU* 3.0 32.3 + - + +
158B LEU* 3.8 4.5 - - - +
160B GLU* 1.3 78.5 - - - +
162B ILE* 1.3 60.4 + - + +
164B ALA* 3.4 1.7 + - - +
165B GLY* 2.8 26.7 + - - -
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Residues in contact with ILE 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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95B ILE* 5.2 0.4 - - + -
127B GLY* 5.3 0.9 - - - -
135B CYS* 4.3 12.6 - - - -
148B ALA* 4.0 15.5 - - + -
158B LEU* 2.9 46.7 + - + +
159B ALA* 3.7 9.2 - - - +
161B ILE* 1.3 75.1 - - + +
163B HIS* 1.3 89.2 + - + +
165B GLY* 3.2 7.2 + - - +
166B GLY 3.3 0.3 + - - -
167B TRP* 2.9 65.3 + - + +
169B SER 3.7 16.8 - - - +
170B ASN* 4.3 5.8 - - + +
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Residues in contact with HIS 163 (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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39B LEU* 3.5 19.6 - - - +
159B ALA* 3.0 27.8 + - + +
160B GLU 4.4 0.7 - - - +
162B ILE* 1.3 88.4 - - + +
164B ALA* 1.3 65.3 + - - +
165B GLY 3.0 1.6 - - - -
166B GLY 3.0 10.2 + - - -
167B TRP 2.9 23.0 + - - +
169B SER 4.0 0.2 - - - -
170B ASN* 3.6 29.9 + - + +
197B CYS 5.2 0.8 + - - -
200B LEU* 3.9 18.2 - - + -
201B VAL* 3.8 17.6 - - + +
204B TYR* 3.8 22.2 - - + -
211B ILE* 3.4 35.1 - - + +
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Residues in contact with ALA 164 (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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29B GLU 5.4 0.2 - - - +
30B VAL* 4.1 15.9 - - + -
31B ASP 5.3 0.4 - - - +
35B ALA* 3.9 26.7 - - + +
38B TYR* 4.1 3.1 - - - -
39B LEU* 5.5 0.2 - - - +
132B VAL* 3.9 20.2 - - + -
136B ARG* 2.9 31.7 + - - +
160B GLU 3.0 20.3 + - - +
161B ILE 4.0 2.5 - - - +
163B HIS* 1.3 77.2 - - - +
165B GLY* 1.3 56.0 + - - +
166B GLY 3.2 3.2 + - - -
204B TYR* 4.1 3.6 + - - +
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Residues in contact with GLY 165 (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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38B TYR* 4.2 0.3 - - - -
132B VAL* 4.0 3.6 - - - +
135B CYS* 3.6 13.6 - - - +
136B ARG* 3.6 33.9 - - - +
139B LEU* 4.0 4.2 - - - +
161B ILE 2.8 15.0 + - - -
162B ILE 3.3 6.5 - - - -
163B HIS 3.0 0.4 - - - -
164B ALA* 1.3 76.5 - - - +
166B GLY* 1.3 58.9 + - - +
167B TRP* 3.3 14.1 - - - -
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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
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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