Contacts of the strand formed by residues 150 - 155 (chain K) 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 150 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142K LEU* 3.5 14.2 - - - +
149K THR* 1.3 76.4 - - - +
151K ILE* 1.3 64.3 + - - -
165K ILE* 2.8 40.6 + - - +
293K LEU* 4.7 6.9 - - - +
296K ASN* 3.2 16.8 - - - -
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Residues in contact with ILE 151 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K GLY* 1.3 73.2 - - - -
152K VAL* 1.3 62.9 + - - +
162K THR* 6.2 2.0 - - - -
163K VAL 3.0 13.7 - - - +
164K PRO* 3.7 16.6 - - + -
278K THR* 4.8 20.0 - - + +
281K SER* 5.7 3.1 - - - -
282K ILE* 3.7 34.8 - - + +
293K LEU* 3.5 24.7 - - + +
294K TYR* 5.6 1.8 - - + -
296K ASN 2.8 18.6 + - - +
297K THR* 3.7 19.5 - - + -
298K VAL* 2.9 27.9 + - - +
317K ILE* 6.3 2.5 - - + -
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Residues in contact with VAL 152 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K ALA* 3.5 26.9 - - + +
141K SER* 3.3 22.9 - - - +
142K LEU* 3.9 18.6 - - + -
151K ILE* 1.3 77.4 - - - +
153K MET* 1.3 63.4 + - - +
154K ASP 3.9 0.4 - - - +
161K HIS 3.4 1.6 - - - +
162K THR* 3.3 7.0 - - - -
163K VAL* 2.9 46.5 + - + +
165K ILE* 4.3 4.5 - - + -
298K VAL* 3.4 22.2 - - + +
300K SER* 3.6 15.0 - - - +
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Residues in contact with MET 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K VAL* 1.3 72.2 - - - +
154K ASP* 1.3 86.6 + - - +
155K SER* 3.6 7.6 + - - +
160K THR* 3.7 21.3 - - + -
161K HIS 3.3 11.7 - - - +
162K THR* 3.6 20.0 - - - -
178K LEU* 6.3 0.2 - - + -
274K ILE* 4.1 34.8 - - + -
278K THR* 4.8 7.9 - - + -
298K VAL 2.9 7.6 + - - +
299K LEU* 3.7 30.7 - - + +
300K SER* 2.7 34.8 + - - +
304K THR* 4.4 7.5 - - + +
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Residues in contact with ASP 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K PRO* 5.5 4.9 - - + +
137K GLN* 4.0 29.1 - - - +
138K ALA* 4.4 16.7 + - + +
152K VAL 3.9 1.0 - - - +
153K MET* 1.3 73.4 - - - +
155K SER* 1.3 61.7 + - - +
156K GLY* 3.7 12.6 + - - -
159K VAL* 4.9 1.8 - - - +
160K THR* 3.1 7.3 - - - -
161K HIS* 2.8 52.7 + - + +
300K SER* 3.3 14.5 + - - +
301K GLY* 5.2 2.5 - - - -
339K VAL* 5.2 5.9 - - - +
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Residues in contact with SER 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K MET* 4.2 7.6 - - - -
154K ASP* 1.3 72.4 + - - +
156K GLY* 1.3 61.3 + - - +
160K THR* 3.7 9.6 - - - -
300K SER 2.6 11.6 + - - -
301K GLY* 3.1 1.9 - - - -
302K GLY 3.1 10.4 + - - -
303K THR* 3.0 28.8 + - - -
304K THR* 2.7 47.0 + - - -
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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