Contacts of the strand formed by residues 155 - 167 (chain B) in PDB entry 3LPJ
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 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU* 3.9 37.2 - - + -
146B VAL 3.5 5.4 - - - +
147B SER* 3.0 20.7 + - - +
154B VAL* 1.3 75.9 - - - +
156B VAL* 1.3 65.9 + - - +
204B GLN* 4.7 3.3 - - - +
205B THR* 4.9 4.2 - - - +
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Residues in contact with VAL 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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145B LEU* 3.3 5.5 - - - -
146B VAL* 2.7 42.9 + - - +
154B VAL* 4.4 3.6 - - + -
155B THR* 1.3 79.2 - - - +
157B ARG* 1.3 75.0 + - - +
158B ALA* 3.6 6.0 + - + +
197B PHE* 4.4 14.4 - - + -
200B SER* 3.8 20.9 - - - -
201B LEU* 3.5 37.0 - - + +
204B GLN* 3.5 18.6 - - - +
205B THR* 4.4 9.4 - - + -
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Residues in contact with ARG 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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120B THR* 3.0 44.9 + - - +
122B ARG* 3.4 45.5 - - - +
143B THR* 3.1 31.2 + - + +
144B ASP* 3.4 15.4 - - - +
145B LEU* 3.9 25.4 - - + +
156B VAL* 1.3 74.2 - - - +
158B ALA* 1.3 60.8 + - - +
200B SER* 4.0 2.6 + - - -
204B GLN* 2.9 35.6 + - - +
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Residues in contact with ALA 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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99B PHE* 4.7 0.9 - - + -
143B THR* 3.1 25.5 - - - -
144B ASP 3.0 12.3 + - - +
146B VAL* 4.2 13.5 - - + -
156B VAL* 3.6 5.5 + - + -
157B ARG* 1.3 76.3 - - - +
159B ASN* 1.3 70.9 + - - +
160B ILE* 3.6 2.6 + - - +
197B PHE* 3.7 34.1 - - + -
200B SER* 4.5 9.6 - - - +
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Residues in contact with ASN 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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99B PHE* 3.4 22.5 + - - +
124B LEU* 3.7 12.4 - - + +
141B LEU* 5.6 0.9 - - + -
142B GLY 3.5 4.7 - - - +
143B THR* 3.4 18.4 - - - +
158B ALA* 1.3 76.2 - - - +
160B ILE* 1.3 63.0 + - - +
193B SER 5.2 0.6 + - - -
194B LEU* 3.5 27.5 - - + +
195B GLU* 3.0 50.5 + - - +
197B PHE* 5.8 1.5 + - - +
200B SER* 5.0 2.2 + - - -
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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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81B VAL* 4.3 11.7 - - + -
99B PHE* 3.7 22.2 - - + +
101B VAL* 3.8 33.4 - - + -
113B TYR* 4.1 18.3 - - + +
140B GLU 3.7 0.5 - - - +
141B LEU* 3.7 3.9 - - - -
142B GLY* 2.8 37.5 + - - +
143B THR 5.3 0.2 - - - -
144B ASP* 3.7 31.2 - - + +
146B VAL* 3.9 18.8 - - + -
158B ALA 3.7 6.5 - - - +
159B ASN* 1.3 80.5 - - - +
161B ALA* 1.3 66.4 + - - +
162B ALA* 3.6 2.9 + - - +
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Residues in contact with ALA 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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98B ASN* 5.2 3.4 - - - +
99B PHE 3.0 10.9 + - - +
100B ALA* 3.2 7.5 - - + +
101B VAL 2.9 26.3 + - - -
128B VAL* 3.9 12.3 - - + -
137B TRP* 3.4 37.5 - - + -
140B GLU 3.7 5.2 - - - -
141B LEU* 4.1 9.4 - - + +
160B ILE* 1.3 74.1 - - - +
162B ALA* 1.3 61.8 + - - +
163B ILE 3.4 1.0 + - - -
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Residues in contact with ALA 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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101B VAL* 3.7 8.5 - - - -
103B ALA* 3.5 19.1 - - + -
113B TYR* 4.5 6.7 - - + -
115B ARG* 3.6 33.9 - - - +
139B GLY* 3.1 4.8 - - - -
140B GLU 2.8 38.4 + - - +
160B ILE 3.6 2.1 + - - +
161B ALA* 1.3 68.3 - - - +
163B ILE* 1.3 62.9 + - - +
164B THR* 3.3 5.2 + - - +
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Residues in contact with ILE 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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100B ALA* 3.8 21.8 - - + -
101B VAL* 2.8 29.5 + - - +
102B GLY* 4.0 3.5 - - - -
103B ALA* 3.0 24.9 + - - +
104B ALA* 3.8 4.3 + - - +
137B TRP* 3.7 34.1 - - + -
138B GLU 3.7 4.5 - - - +
139B GLY* 4.2 0.4 - - - -
161B ALA 4.1 0.2 - - - +
162B ALA* 1.3 69.5 - - - +
164B THR* 1.3 62.1 + - - +
165B GLU 3.6 23.3 - - - +
166B SER* 4.2 8.1 - - - +
169B PHE* 3.7 30.1 - - + -
170B PHE* 4.0 13.5 - - + -
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Residues in contact with THR 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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299A LYS* 5.2 3.5 + - - -
303A GLU* 5.0 1.6 - - - +
103B ALA* 5.2 1.6 - - + -
104B ALA* 4.6 18.9 - - + +
115B ARG* 4.3 13.2 - - - +
138B GLU* 3.0 13.8 + - - +
139B GLY* 4.0 6.6 - - - -
140B GLU* 4.0 27.3 + - + +
162B ALA 3.3 10.5 + - - +
163B ILE* 1.3 77.5 - - - +
165B GLU* 1.3 74.5 + - - +
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Residues in contact with GLU 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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299A LYS* 5.5 1.8 - - - +
303A GLU* 3.7 52.2 - - - +
307A LYS* 6.1 1.6 - - - +
137B TRP* 3.3 2.6 - - - +
138B GLU* 2.8 54.0 + - + +
163B ILE* 3.6 3.2 - - - +
164B THR* 1.3 89.4 + - - +
166B SER* 1.3 65.1 + - - +
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Residues in contact with SER 166 (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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299A LYS* 5.7 3.3 + - - +
300A LYS* 4.5 14.0 - - - +
303A GLU* 4.7 6.4 + - - +
106B HIS* 3.6 18.5 + - - -
136B LYS 3.5 10.5 - - - -
137B TRP* 4.0 9.2 - - - +
163B ILE* 4.2 1.3 - - - +
165B GLU* 1.3 77.0 - - - +
167B ASP* 1.3 62.2 + - - +
168B LYS 4.2 0.2 - - - -
169B PHE* 4.1 9.8 + - - -
170B PHE* 3.5 33.8 + - - -
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Residues in contact with ASP 167 (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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276A MET* 4.8 11.3 - - - +
300A LYS* 2.8 36.1 + - + +
135B GLY* 3.4 1.7 - - - -
136B LYS* 2.9 61.1 + - + +
166B SER* 1.3 74.7 - - - +
168B LYS* 1.3 94.7 + - - +
169B PHE 3.2 0.2 - - - -
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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