Contacts of the helix formed by residues 154 - 162 (chain J) in PDB entry 6LTJ
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 154 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17J ASP* 5.0 8.1 - - - +
123J SER* 2.8 18.6 + - - +
124J GLU* 3.2 26.0 + - - +
125J ALA* 4.0 7.3 - - - +
126J PRO* 5.4 0.9 - - - +
153J LYS* 1.3 68.7 - - - +
155J ALA* 1.3 63.3 + - - +
157J LEU* 3.1 5.1 + - - +
158J THR* 2.9 35.3 + - - +
171J ASP* 4.8 8.0 + - - -
180J ILE* 4.7 8.0 - - - +
393J SER* 3.4 24.5 - - - +
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Residues in contact with ALA 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PRO* 5.5 3.0 - - + +
153J LYS* 3.1 3.3 - - + +
154J THR* 1.3 79.2 + - - +
156J VAL* 1.3 58.0 + - - +
158J THR* 3.6 2.4 + - - +
159J ALA* 2.9 32.3 + - - +
169J ILE* 3.3 19.8 - - + +
180J ILE* 3.7 30.0 - - + +
182J VAL* 4.3 3.8 - - + -
187J VAL* 3.7 26.0 - - + -
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Residues in contact with VAL 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J CYS* 3.7 20.9 - - + -
153J LYS* 3.1 16.3 + - + +
155J ALA* 1.3 74.9 - - - +
157J LEU* 1.3 63.2 + - + +
159J ALA* 4.3 2.2 - - - -
160J PHE* 2.9 58.0 + - + -
182J VAL* 3.6 24.2 - - + -
185J GLY* 4.0 20.2 - - - +
186J TYR* 4.7 0.2 - - - -
187J VAL* 3.9 14.6 - - + -
400J LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J VAL* 5.6 2.0 - - + -
17J ASP* 6.5 1.1 - - + -
121J LEU* 5.3 7.2 - - + -
122J MET 5.6 0.4 - - - -
123J SER* 3.7 24.2 - - - +
152J CYS* 3.6 24.0 - - - -
153J LYS 3.6 1.8 + - - +
154J THR 3.1 9.0 + - - +
156J VAL* 1.3 84.5 - - + +
158J THR* 1.3 58.9 + - - +
160J PHE* 3.8 1.4 - - - -
161J ALA 2.9 23.6 + - - -
393J SER* 3.2 29.8 - - - +
394J TRP* 5.2 1.3 - - - -
396J GLY* 3.2 30.9 - - - +
397J GLY* 3.6 15.9 - - - +
400J LEU* 4.3 16.6 - - + -
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Residues in contact with THR 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J THR* 2.9 20.5 + - - +
155J ALA 3.7 4.7 - - - +
157J LEU* 1.3 77.1 - - - +
159J ALA* 1.3 61.5 + - - +
161J ALA* 3.7 1.1 - - - +
162J ASN* 2.9 30.3 + - - +
169J ILE* 3.7 31.2 - - + -
349J ILE* 4.4 9.9 - - + +
350J VAL 5.3 0.2 + - - -
351J ALA* 4.5 5.2 - - + +
392J SER* 2.3 40.4 + - - -
393J SER* 3.7 12.5 - - - +
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Residues in contact with ALA 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155J ALA 2.9 20.4 + - - +
156J VAL* 3.8 4.9 - - - +
157J LEU 3.2 0.2 - - - -
158J THR* 1.3 76.8 - - - +
160J PHE* 1.3 65.0 + - + +
162J ASN* 3.3 4.7 + - - +
163J GLY 3.2 4.2 + - - -
164J ARG* 2.9 37.4 + - + +
165J SER 5.2 0.2 - - - +
167J GLY* 5.5 1.1 - - - -
169J ILE* 4.0 5.4 - - + -
182J VAL* 3.8 25.1 - - + -
349J ILE* 4.8 13.0 - - + -
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Residues in contact with PHE 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476I LEU* 4.7 5.2 - - + -
477I ASN* 5.7 0.4 - - - -
480I LEU* 3.5 42.2 - - + -
484I LYS* 4.2 12.9 - - - +
156J VAL* 2.9 42.2 + - + +
157J LEU 4.0 2.2 - - - +
159J ALA* 1.3 78.0 - - + +
161J ALA* 1.3 58.8 + - - +
163J GLY* 2.8 20.0 + - - +
164J ARG 3.2 20.4 - - - +
165J SER* 3.9 24.2 - - - -
182J VAL* 5.8 0.9 - - + -
184J ASP 5.0 0.2 - - - -
185J GLY* 3.6 28.5 - - - -
399J ILE* 4.8 8.3 - - + +
400J LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491I ARG* 5.6 3.8 + - - -
157J LEU 2.9 18.6 + - - +
158J THR* 3.8 4.3 - - - +
160J PHE* 1.3 77.6 - - - +
162J ASN* 1.3 60.9 - - - +
163J GLY 3.2 1.4 + - - -
392J SER* 3.3 26.2 - - - +
395J ILE* 3.8 17.5 - - + +
396J GLY* 3.4 14.7 - - - +
399J ILE* 4.7 4.7 - - - -
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Residues in contact with ASN 162 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J THR* 2.9 17.6 + - - +
159J ALA 3.3 4.2 + - - +
160J PHE 3.2 0.4 - - - -
161J ALA* 1.3 78.0 - - - +
163J GLY* 1.3 62.1 + - - +
164J ARG* 3.3 10.8 + - - +
349J ILE* 3.4 41.7 - - + +
350J VAL 4.7 0.2 + - - -
381J ILE* 3.5 36.9 - - + +
383J ASN* 3.9 19.3 + - - +
389J ARG* 4.0 9.7 - - - +
392J SER* 5.6 4.2 - - - -
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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