Contacts of the strand formed by residues 142 - 152 (chain B) in PDB entry 1N8Z
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 142 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 5.0 3.4 - - + -
137B SER 3.7 0.9 - - - +
138B THR* 3.1 8.6 - - - -
139B SER* 3.1 40.0 + - - +
140B GLY 3.1 5.1 + - - -
141B GLY* 1.3 80.3 + - - +
143B ALA* 1.3 60.8 + - - +
190B THR* 2.7 40.6 - - + -
191B VAL 3.4 8.3 + - - +
192B PRO* 4.9 0.9 - - - +
193B SER* 3.8 1.3 + - - -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 5.7 0.2 - - - -
133B PRO* 4.4 9.4 - - + -
137B SER 3.4 4.3 - - - +
138B THR* 3.7 16.6 - - + -
142B THR* 1.3 78.5 - - - +
144B ALA* 1.3 59.8 + - - +
189B VAL 3.7 0.5 - - - +
190B THR* 3.2 3.1 - - - +
191B VAL* 2.7 53.4 + - + +
193B SER* 4.1 3.5 - - - +
196B LEU* 3.8 26.0 - - + -
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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
----------------------------------------------------------
116A PHE* 3.8 37.9 - - + -
118A PHE* 3.4 14.8 - - + -
135A LEU* 4.0 9.0 - - + -
133B PRO* 3.6 6.2 - - - +
137B SER* 2.9 32.1 + - - +
143B ALA* 1.3 74.4 - - - +
145B LEU* 1.3 62.9 + - - +
189B VAL 3.3 8.5 - - - +
190B THR* 4.4 4.7 - - + +
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Residues in contact with LEU 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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118A PHE* 4.1 4.9 - - - -
131B LEU* 3.5 17.7 - - - +
133B PRO* 3.6 28.0 - - + -
144B ALA* 1.3 76.3 - - - +
146B GLY* 1.3 58.1 + - - +
161B TRP* 3.7 18.8 - - + -
188B VAL* 3.2 6.4 - - - +
189B VAL* 2.6 69.2 + - + +
191B VAL* 4.3 15.0 - - + -
196B LEU* 4.5 2.5 - - + -
201B TYR* 4.0 33.2 - - + -
218B VAL* 4.1 9.4 - - + +
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Residues in contact with GLY 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 2.7 39.6 + - - +
145B LEU* 1.3 80.8 - - - +
147B CYS* 1.3 56.9 + - - -
161B TRP* 3.6 15.7 - - - -
187B SER 3.0 13.9 - - - -
188B VAL* 3.8 0.7 - - - -
218B VAL* 3.5 12.3 - - - +
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Residues in contact with CYS 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 4.1 13.5 - - + -
129B PHE 3.4 8.5 - - - +
131B LEU* 3.6 1.7 - - - +
146B GLY* 1.3 78.6 - - - -
148B LEU* 1.3 60.2 + - - +
149B VAL* 4.0 6.2 + - + +
161B TRP* 3.9 1.5 - - + -
186B SER* 3.0 7.7 + - - -
187B SER* 2.8 35.6 + - - +
203B CYS* 2.1 52.0 - - + -
205B VAL* 4.8 1.1 - - + -
216B LYS* 4.4 4.0 - - - -
218B VAL* 3.8 15.0 - - - -
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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
----------------------------------------------------------
124A GLN* 4.1 6.1 - - - +
131A SER* 3.6 33.2 - - - +
133A VAL* 4.3 17.5 - - + -
178A THR* 4.8 7.4 - - + +
127B SER 3.7 0.7 - - - +
128B VAL* 3.2 7.1 - - - +
129B PHE* 2.8 62.9 + - + +
131B LEU* 4.1 12.9 - - + +
147B CYS* 1.3 73.0 - - - +
149B VAL* 1.3 61.3 + - - +
150B LYS* 3.8 9.6 - - + -
184B SER* 4.3 12.1 - - - +
185B LEU 3.8 14.8 - - - +
186B SER* 3.9 11.2 - - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PRO* 3.6 27.4 - - + -
127B SER 3.5 2.9 - - - +
128B VAL* 4.2 3.6 - - + +
147B CYS* 4.5 6.1 - - + +
148B LEU* 1.3 78.9 - - - +
150B LYS* 1.3 57.4 + - - +
152B TYR* 4.0 12.2 - - + -
157B VAL* 4.2 8.3 - - + -
159B VAL* 4.1 4.3 - - + -
184B SER* 3.5 4.3 + - - -
185B LEU* 2.9 55.3 + - + +
205B VAL* 3.8 42.2 - - + -
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Residues in contact with LYS 150 (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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124A GLN* 4.0 9.4 - - - +
129A THR* 3.6 23.7 + - + +
131A SER* 3.9 16.2 - - - +
180A THR* 4.3 9.1 - - - +
126B PRO* 3.1 7.7 - - - +
127B SER* 2.8 40.8 + - - +
129B PHE* 3.9 19.7 - - + -
148B LEU* 3.8 15.9 - - + -
149B VAL* 1.3 73.9 - - - +
151B ASP* 1.3 92.7 + - + +
152B TYR 3.8 1.1 - - - -
178B GLN* 3.6 25.7 - - - +
183B TYR 4.1 0.2 - - - -
184B SER* 3.7 14.8 - - - +
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Residues in contact with ASP 151 (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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129A THR* 6.0 0.3 - - - -
124B LYS* 3.7 11.4 - - + +
125B GLY 3.0 20.8 - - - +
127B SER* 4.9 7.8 + - - +
150B LYS* 1.3 103.5 + - + +
152B TYR* 1.3 58.6 + - - +
178B GLN* 3.3 18.8 + - - +
180B SER* 4.5 1.9 + - - -
182B LEU* 3.9 30.7 - - + +
183B TYR 3.1 12.0 + - - -
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Residues in contact with TYR 152 (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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124B LYS* 3.0 12.8 - - - +
126B PRO* 3.7 18.6 - - + -
149B VAL* 4.0 28.3 - - + -
151B ASP* 1.3 77.0 - - - +
153B PHE* 1.3 60.5 + - - +
154B PRO 3.4 20.6 - - - -
155B GLU* 2.5 35.6 + - - -
157B VAL* 3.6 30.8 - - + +
175B ALA* 3.2 15.1 - - - +
182B LEU* 4.0 2.9 - - - +
183B TYR* 2.7 70.2 + - + +
184B SER* 4.0 3.8 - - - -
185B LEU* 4.1 8.0 - - + +
207B HIS* 4.0 4.3 - + - +
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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