Contacts of the strand formed by residues 156 - 161 (chain B) in PDB entry 1CP3
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 LYS 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114B PHE* 3.6 11.0 - - + -
143B PHE* 3.0 34.8 + - + +
145B GLY* 4.7 5.6 - - - +
151B LEU* 2.9 51.7 + - + -
152B THR* 4.1 6.3 - - - +
153B GLY 4.4 0.6 - - - +
154B LYS 2.9 16.4 + - - +
155B PRO* 1.3 71.6 - - - +
157B LEU* 1.3 64.0 + - - +
158B PHE* 3.9 11.3 - - + -
191B ALA 3.7 16.0 + - - -
192B ASP* 2.9 12.9 + - - +
193B PHE* 3.5 38.2 - - + -
194B LEU 3.1 23.4 + - - +
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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
----------------------------------------------------------
78B PHE* 6.2 0.4 - - + -
83B TYR* 4.7 5.6 - - - +
113B SER* 5.1 3.6 - - - -
114B PHE* 2.8 14.1 + - - +
115B VAL* 3.4 30.7 - - + -
116B CYS* 2.9 26.3 + - - +
155B PRO* 4.2 21.1 - - + +
156B LYS* 1.3 77.4 - - - +
158B PHE* 1.3 66.4 + - - +
159B ILE* 4.2 6.3 - - + -
194B LEU* 3.7 27.6 - - + +
232B PHE* 4.0 19.5 - - + -
269B LEU* 4.5 2.7 - - + -
273B LEU* 4.0 25.4 - - + -
275B PHE* 4.6 10.5 - - + -
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Residues in contact with PHE 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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114B PHE* 4.0 8.3 - + - -
116B CYS* 3.4 32.8 - - + -
118B LEU* 4.7 10.8 - - + -
136B LEU* 5.7 0.2 - - + -
139B ILE* 4.5 7.4 - - + -
140B THR* 3.8 25.6 - - + -
143B PHE* 3.6 32.3 - + - -
156B LYS* 3.9 16.8 - - + -
157B LEU* 1.3 79.1 - - - +
159B ILE* 1.3 62.8 + - - +
160B ILE* 4.1 11.2 - - + +
193B PHE* 3.6 29.8 - + - -
194B LEU* 2.9 12.9 + - - +
195B TYR* 3.5 17.8 - + + -
196B ALA* 2.9 26.9 + - - +
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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
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74B LEU* 5.5 0.9 - - + -
78B PHE* 4.0 18.8 - - + -
115B VAL* 3.9 27.1 - - + -
116B CYS 2.9 9.9 + - - +
117B VAL* 3.4 14.6 - - + +
118B LEU* 2.9 27.0 + - - +
157B LEU* 5.1 6.7 - - + -
158B PHE* 1.3 76.8 - - - +
160B ILE* 1.3 66.6 + - - +
161B GLN 4.3 0.2 - - - -
194B LEU* 6.1 0.4 - - + -
196B ALA* 3.5 15.3 - - + +
215B PHE* 3.6 26.5 - - + -
216B ILE* 4.2 13.2 - - + -
219B LEU* 3.8 20.2 - - + -
232B PHE* 5.4 9.6 - - + -
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Residues in contact with ILE 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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118B LEU* 3.7 19.7 - - + +
127B ILE* 4.2 24.9 - - + -
136B LEU* 4.4 20.4 - - + -
140B THR* 6.4 0.2 - - + -
158B PHE* 4.2 22.7 - - + +
159B ILE* 1.3 82.4 - - - +
161B GLN* 1.3 64.2 + - - +
162B ALA* 4.0 6.4 + - + +
164B ARG* 6.4 1.8 - - + -
195B TYR* 4.7 6.3 - - + -
196B ALA 2.9 10.8 + - - +
197B TYR* 3.7 36.0 - - + -
198B SER* 2.9 33.2 + - - -
215B PHE* 4.7 2.7 - - - -
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Residues in contact with GLN 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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64B ARG* 4.2 9.6 - - - +
118B LEU 3.1 9.6 + - - +
119B LEU* 3.6 21.5 - - + +
120B SER 3.1 21.3 + - - +
159B ILE* 4.3 0.6 - - - +
160B ILE* 1.3 70.3 - - - +
162B ALA* 1.3 71.4 + - - +
198B SER* 3.4 15.2 - - - -
205B SER* 2.7 30.8 + - - -
206B TRP 4.1 7.1 + - - +
213B SER* 3.2 35.7 + - - +
215B PHE* 3.7 7.3 - - + +
216B ILE* 4.2 9.6 - - + -
261B GLN* 4.9 0.2 + - - -
993D ASP* 2.9 27.8 + - - +
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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