Contacts of the strand formed by residues 147 - 155 (chain K) in PDB entry 5LS6
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 PHE 147 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J LEU* 4.3 7.6 - - + -
97K PHE* 3.9 6.6 - - - -
116K VAL* 3.8 21.4 - - + -
117K GLY 3.9 12.6 + - - +
118K SER 3.0 7.8 + - - +
119K ASN 3.3 22.2 - - - -
120K ARG* 3.5 30.5 - - - -
121K VAL* 4.3 3.4 - - + -
140K ASP* 3.5 28.0 - - + -
145K GLU* 3.7 21.3 - - + -
146K ASN* 1.3 82.8 - - - +
148K TYR* 1.3 60.9 + - - +
165K VAL* 3.4 34.8 - - + -
166K ALA* 3.5 21.1 - - - +
167K GLY* 4.0 0.4 - - - -
171K ILE 5.0 0.9 - - - -
173K ARG* 4.0 10.8 - - + -
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Residues in contact with TYR 148 (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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97K PHE* 3.3 33.3 - + - +
98K GLY* 4.1 0.3 - - - -
116K VAL* 4.3 3.1 - - - -
146K ASN* 3.4 31.0 + - - -
147K PHE* 1.3 78.3 - - - +
149K THR* 1.3 59.7 + - - +
166K ALA 2.8 4.9 + - - -
167K GLY* 3.7 0.9 - - - -
168K SER* 3.4 40.7 - - - -
192K ALA* 3.9 11.0 - - + -
193K ILE 3.7 22.4 - - - +
194K ASN* 4.0 11.2 - - - -
365K TYR* 3.2 24.2 + - - +
367K ARG* 4.7 0.9 + - - -
7T M3L 3.7 45.8 - - - -
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Residues in contact with THR 149 (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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98K GLY* 4.9 3.7 - - - -
116K VAL* 3.7 11.4 - - - +
147K PHE 3.8 0.4 - - - -
148K TYR* 1.3 80.8 - - - +
150K CYS* 1.3 74.2 + - - +
165K VAL* 3.4 3.1 - - - +
166K ALA 3.2 26.1 + - - +
193K ILE* 4.1 6.7 - - + +
194K ASN 3.8 12.1 - - - -
195K GLU* 3.6 18.6 + - - +
196K LEU* 3.6 45.6 + - + +
365K TYR* 4.6 0.2 - - - -
367K ARG* 5.0 4.3 + - - -
415K GLN* 5.8 0.7 + - - -
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Residues in contact with CYS 150 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K GLY* 4.4 2.8 - - - -
99K VAL 4.4 5.6 - - - -
100K GLN* 3.3 33.3 - - - +
114K ALA* 4.3 17.7 - - - -
116K VAL* 3.7 31.2 - - + -
149K THR* 1.3 85.9 + - - +
151K ALA* 1.3 63.4 + - - +
163K LEU* 3.9 14.4 - - + -
164K ALA 2.9 13.9 - - - +
165K VAL* 4.1 2.0 - - + -
196K LEU* 4.7 2.7 - - - +
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Residues in contact with ALA 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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100K GLN* 4.5 7.4 - - + -
150K CYS* 1.3 75.2 - - - +
152K TRP* 1.3 59.4 + - - +
163K LEU* 3.7 6.5 - - - +
164K ALA* 3.0 30.7 + - - +
196K LEU* 3.5 27.5 - - + +
197K LYS* 4.4 6.3 - - + -
198K PHE* 3.3 27.8 - - + +
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Residues in contact with TRP 152 (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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100K GLN* 2.7 35.9 + - + +
101K PHE 3.5 20.0 - - - +
102K ASN* 3.5 41.7 - - + +
103K TRP 5.1 0.4 - - - +
104K HIS* 3.4 24.0 + - + -
112K VAL* 4.7 7.0 - - + -
113K PHE* 4.3 4.7 - - - -
114K ALA* 3.7 26.1 - - + +
123K LEU* 4.2 23.1 - - + -
151K ALA* 1.3 72.5 - - - +
153K THR* 1.3 62.6 - - - +
161K PRO* 4.1 19.3 - - + -
162K LEU 3.4 17.7 - - - -
163K LEU* 3.9 21.6 - - + +
177K PRO* 4.6 9.0 - - + -
198K PHE* 3.5 13.1 - - - +
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Residues in contact with THR 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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104K HIS* 3.6 16.3 + - - -
152K TRP* 1.3 75.7 - - - +
154K TYR* 1.3 71.6 + - - +
161K PRO* 3.6 4.5 - - - +
162K LEU* 2.7 49.3 + - + +
174K ILE* 6.0 0.7 - - + -
198K PHE* 3.4 38.4 - - + +
203K PRO* 2.5 34.4 + - - +
220K ILE* 4.2 4.9 - - + -
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Residues in contact with TYR 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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63J ARG* 2.8 48.1 + - + +
65J ILE* 4.2 24.7 - - + -
104K HIS* 3.5 32.3 - + + -
153K THR* 1.3 83.4 + - - +
155K ASP* 1.3 57.6 + - - +
156K SER* 3.4 37.7 + - - -
159K SER* 5.4 0.2 - - - -
160K HIS 3.1 19.5 - - - +
161K PRO* 4.3 2.0 - - + -
162K LEU* 3.6 10.7 - - - +
203K PRO* 3.5 41.8 - - + +
204K ASN* 4.8 3.1 - - - +
220K ILE* 5.9 0.5 - - - +
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Residues in contact with ASP 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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154K TYR* 1.3 68.6 - - - +
156K SER* 1.3 58.4 + - - +
157K ASN* 3.1 25.0 + - - +
158K THR* 3.1 33.5 + - - +
159K SER* 2.7 36.0 + - - -
160K HIS* 2.9 15.4 + - + +
162K LEU* 3.4 19.1 - - + +
183K ILE* 6.2 2.0 - - + +
204K ASN* 5.2 6.0 - - - +
221K GLN* 5.4 2.3 - - - +
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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