Contacts of the strand formed by residues 135 - 141 (chain A) in PDB entry 1LIK
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 GLU 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ARG* 3.4 35.7 - - + -
42A GLY* 3.8 18.4 - - - +
130A LEU 3.7 0.2 - - - +
131A ILE* 3.6 6.0 - - - +
132A ASN 3.2 31.2 + - - +
133A GLU* 4.5 5.2 - - + -
134A LYS* 1.3 86.1 - - + +
136A ARG* 1.3 61.1 + - - +
137A THR* 5.2 0.2 + - - -
313A THR* 4.4 6.7 + - - -
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Residues in contact with ARG 136 (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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42A GLY* 3.0 42.7 + - - -
43A ASP 4.2 3.6 + - - -
44A ALA* 4.4 8.9 - - - +
129A VAL* 4.8 2.9 - - + -
130A LEU 3.4 4.9 - - - +
131A ILE* 4.6 6.3 - - + -
134A LYS 4.0 0.2 + - - -
135A GLU* 1.3 76.0 + - - +
137A THR* 1.3 62.6 + - - +
138A LEU* 3.6 29.4 - - - +
169A TYR* 5.1 2.2 + - - -
198A SER 5.5 2.4 + - - -
225A GLU* 5.4 3.4 + - - -
312A ASP* 5.8 0.2 - - + -
313A THR* 3.8 16.8 + - - +
314A ASN* 3.4 50.0 - - + +
315A GLY 4.7 1.6 - - - +
699A ADN 4.9 2.6 + - - -
999A SO4 3.4 35.2 + - - -
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Residues in contact with THR 137 (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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34A LEU* 4.6 6.3 - - + +
39A LEU* 4.2 33.0 - - + -
40A LYS 3.5 19.3 - - - +
41A ARG* 3.3 10.9 - - - +
42A GLY 2.9 21.8 + - - -
43A ASP* 3.5 9.9 - - + +
45A THR* 6.3 0.4 - - + -
128A ALA 3.1 4.2 - - - +
129A VAL 3.5 0.7 - - - -
130A LEU* 2.6 50.9 + - + +
132A ASN* 6.0 0.7 - - - +
135A GLU 5.2 0.3 + - - -
136A ARG* 1.3 71.3 - - - +
138A LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 138 (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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43A ASP 3.0 9.4 + - - +
44A ALA* 3.5 18.7 - - + -
45A THR* 3.0 27.2 + - - +
127A CYS* 3.7 22.0 - - - -
128A ALA 3.6 0.9 - - - -
129A VAL* 4.2 12.1 - - + -
136A ARG* 3.6 39.0 - - - +
137A THR* 1.3 77.3 - - - +
139A CYS* 1.3 61.0 + - - +
140A THR* 4.1 0.9 - - - -
169A TYR* 4.3 4.3 - - - +
314A ASN* 3.9 21.3 - - - +
699A ADN 3.9 38.4 - - + +
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Residues in contact with CYS 139 (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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39A LEU* 4.3 19.3 - - + -
45A THR* 3.6 5.4 - - - -
46A LEU 4.7 0.4 - - - -
47A ALA* 3.7 34.3 - - - -
51A GLN* 4.0 21.1 - - - -
54A ILE* 4.7 7.9 - - + -
55A TYR* 3.0 10.1 + - - -
127A CYS* 3.5 0.6 - - - -
128A ALA* 2.7 48.4 + - + +
130A LEU* 4.5 6.1 - - + -
137A THR 3.9 0.2 + - - -
138A LEU* 1.3 72.5 - - - +
140A THR* 1.3 59.7 + - - +
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Residues in contact with THR 140 (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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22A ILE* 3.9 18.2 - - + -
45A THR 2.9 16.7 + - - -
46A LEU* 3.3 15.3 - - + +
47A ALA* 2.5 30.0 + - - +
55A TYR* 3.2 6.5 - - - -
126A THR 3.6 7.6 - - - +
127A CYS* 3.5 7.9 - - + -
138A LEU 4.8 0.7 - - - -
139A CYS* 1.3 77.2 + - - +
141A HIS* 1.3 61.9 + - - +
142A LEU* 3.8 12.6 - - + +
699A ADN 2.8 47.2 + - + +
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Residues in contact with HIS 141 (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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47A ALA* 5.1 4.3 - - + -
52A MET* 3.2 39.2 - - + +
55A TYR* 3.6 21.8 - - + +
123A SER* 4.6 11.3 + - - -
124A THR 5.6 1.2 + - - -
125A GLY* 3.3 1.8 - - - -
126A THR* 3.0 37.1 + - + +
140A THR* 1.3 75.7 - - - +
142A LEU* 1.3 65.0 + - - +
143A GLY* 3.2 19.2 + - - -
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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