Contacts of the strand formed by residues 160 - 165 (chain A) in PDB entry 1LTQ
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 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS 4.7 1.6 - - - +
159A PRO* 1.3 74.8 - - - +
161A ALA* 1.3 59.9 + - - +
204A GLY 4.5 2.7 + - - +
205A TYR* 3.6 29.2 - - + +
206A GLN* 2.9 23.7 + - - +
271A ASP* 3.1 30.3 - - + +
273A LYS* 3.1 34.2 - - + +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 1.3 77.1 - - - +
162A VAL* 1.3 66.9 + - - +
163A ILE* 6.0 0.4 - - + -
205A TYR* 4.0 2.2 - - - -
206A GLN* 3.1 27.4 - - + +
208A VAL* 4.3 9.4 - - + -
266A ILE* 6.1 0.4 - - + -
270A PHE* 4.0 24.7 - - + -
271A ASP 3.0 7.4 + - - +
272A VAL* 3.3 8.1 - - + +
273A LYS* 2.9 26.7 + - - +
274A LEU 3.7 1.4 + - - -
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA* 1.3 78.3 - - - +
163A ILE* 1.3 68.4 + - - +
164A PHE* 3.5 32.2 + - + -
200A TYR* 3.9 23.6 - - + -
205A TYR* 3.6 29.8 - - + -
206A GLN 3.0 7.6 + - - +
207A ILE* 3.8 2.8 - - + -
208A VAL* 3.0 24.9 + - - +
274A LEU* 3.3 36.3 - - + +
276A ILE* 4.3 2.0 - - + -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 5.6 0.4 - - + -
162A VAL* 1.3 75.7 - - - +
164A PHE* 1.3 63.1 + - - +
208A VAL* 3.3 16.6 - - + +
210A VAL* 3.6 29.6 - - + -
262A PHE* 3.9 16.8 - - + -
266A ILE* 4.3 12.6 - - + -
272A VAL* 3.7 27.4 - - + -
274A LEU 2.7 12.2 + - - +
275A ALA* 3.2 7.4 - - + -
276A ILE* 2.7 35.6 + - - +
286A TRP* 3.8 35.7 - - + -
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Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL* 3.5 31.2 - - + -
163A ILE* 1.3 82.4 - - - +
165A ASP* 1.3 63.7 + - - +
169A THR* 4.6 1.1 - - + -
170A LEU* 3.8 28.5 - - + -
193A VAL* 3.8 24.2 - - + -
196A LEU* 3.9 16.8 - - + -
197A SER* 3.4 38.4 - - - -
200A TYR* 4.2 4.9 - + - -
207A ILE* 4.1 15.3 - - + -
208A VAL 2.8 12.0 + - - +
209A VAL* 3.3 10.2 - - + +
210A VAL 2.8 26.7 + - - -
276A ILE* 3.8 21.1 - - + -
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PHE* 1.3 77.3 - - - +
166A VAL* 1.3 70.8 + - - +
167A ASP* 2.9 28.1 + - - +
169A THR* 3.3 22.3 + - - +
170A LEU* 3.4 14.3 - - - +
210A VAL* 3.1 13.1 - - + +
211A SER* 3.8 6.1 + - - -
212A GLY 4.4 1.4 + - - -
258A LYS* 2.7 27.8 + - - +
276A ILE 3.2 8.6 + - - +
277A ASP* 3.2 34.4 - - - +
278A ASP* 4.1 1.2 - - - +
279A ARG* 5.8 0.5 - - - +
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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