Contacts of the strand formed by residues 167 - 172 (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 GLY 167 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159J ALA* 5.5 0.9 - - - -
164J ARG* 5.5 0.7 - - - -
166J THR* 1.3 76.7 - - - +
168J LEU* 1.3 59.8 + - - -
169J ILE* 4.8 0.2 - - - -
181J PRO 3.7 0.3 - - - -
182J VAL* 2.8 47.1 + - - +
344J LEU* 3.3 13.3 - - - +
347J SER* 3.3 15.6 + - - -
349J ILE* 5.1 7.0 - - - -
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Residues in contact with LEU 168 (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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167J GLY* 1.3 74.7 - - - +
169J ILE* 1.3 60.7 + - - +
170J LEU* 5.1 1.8 - - + +
179J ALA* 4.4 4.7 - - + -
180J ILE 3.3 34.5 - - - +
181J PRO* 3.8 11.0 - - + -
329J VAL* 4.1 31.9 - - + +
332J SER* 4.4 15.5 - - - +
333J VAL* 5.4 7.4 - - + -
344J LEU* 4.0 22.0 - - + +
345J TYR* 6.2 2.9 - - + -
347J SER 2.7 15.2 + - - +
348J VAL* 3.4 13.5 - - + +
349J ILE* 2.5 35.6 + - - +
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Residues in contact with ILE 169 (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* 3.3 34.5 - - + +
158J THR* 3.7 27.8 - - + -
159J ALA* 4.0 2.9 - - + -
167J GLY 4.8 0.2 - - - -
168J LEU* 1.3 77.1 - - - +
170J LEU* 1.3 65.6 + - - +
171J ASP* 3.7 4.3 - - + +
178J THR 3.8 0.2 - - - +
179J ALA* 3.4 3.6 - - - -
180J ILE* 2.9 53.0 + - + +
182J VAL* 3.7 26.2 - - + -
349J ILE* 3.3 23.1 - - + +
351J ALA* 3.8 19.1 - - + -
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Residues in contact with LEU 170 (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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168J LEU* 5.9 2.0 - - + -
169J ILE* 1.3 73.3 - - - +
171J ASP* 1.3 61.6 - - - +
172J SER* 3.6 2.2 + - - -
177J THR* 5.3 2.5 - - - +
178J THR 3.4 15.3 - - - +
179J ALA* 3.8 19.1 - - + -
325J VAL* 3.7 30.1 - - + -
328J VAL* 4.7 4.0 - - + -
329J VAL* 3.8 26.2 - - + -
348J VAL* 5.7 6.3 - - + -
349J ILE 2.5 15.1 + - - +
350J VAL* 3.8 8.8 - - + +
351J ALA 2.7 32.5 + - - +
360J PHE* 5.6 3.6 - - + -
364J LEU* 4.1 24.7 - - + -
368J LEU* 5.9 0.4 - - + -
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Residues in contact with ASP 171 (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* 4.8 8.3 + - - -
169J ILE* 3.7 4.8 + - + +
170J LEU* 1.3 74.9 - - - +
172J SER* 1.3 53.1 + - - +
173J GLY* 2.9 29.7 + - - -
176J HIS* 2.9 30.9 + - - -
177J THR* 2.6 24.9 + - - -
178J THR* 2.9 37.2 + - - +
180J ILE* 4.9 8.7 - - + +
351J ALA* 3.3 13.5 - - + +
352J GLY* 4.7 6.4 - - - -
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Residues in contact with SER 172 (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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170J LEU* 4.8 2.9 - - - -
171J ASP* 1.3 73.8 + - - +
173J GLY* 1.3 59.0 + - - +
177J THR* 3.5 12.1 - - - -
350J VAL* 6.2 0.4 - - - -
351J ALA 2.5 18.1 + - - -
352J GLY* 3.7 0.9 - - - -
353J GLY 2.5 25.1 + - - -
354J ASN* 2.9 43.2 + - - +
355J THR* 3.7 4.0 + - - +
360J PHE* 5.2 9.6 - - - -
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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