Contacts of the strand formed by residues 135 - 143 (chain D) in PDB entry 3SKU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D VAL* 5.3 5.0 - - - +
33D VAL* 3.5 7.9 - - - +
68D GLN* 5.4 0.9 - - - +
75D LYS* 5.4 4.2 + - - -
123D ILE* 4.2 29.6 - - + +
124D CYS 3.1 13.5 - - - +
125D GLU* 3.8 20.5 - - + +
133D ASN* 5.8 0.9 + - - +
134D ARG* 1.3 79.3 - - - +
136D SER* 1.3 67.5 + - - +
137D GLN* 5.0 5.2 + - + -
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Residues in contact with SER 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 5.5 4.7 - - - -
33D VAL* 2.9 25.9 + - - +
35D VAL* 3.3 22.8 + - - +
67D TRP* 5.5 0.2 - - - -
123D ILE* 3.4 7.3 - - - +
124D CYS* 3.0 30.3 + - - +
135D GLU* 1.3 77.0 - - - +
137D GLN* 1.3 67.7 + - - +
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 4.3 4.6 - - - +
36D ASN 3.1 14.2 - - - +
37D ASP* 3.9 3.5 - - - +
70D SER* 6.1 1.2 - - - -
121D VAL* 2.9 26.9 - - + +
122D TYR 3.0 8.3 - - - +
123D ILE* 3.9 25.1 - - + +
135D GLU* 5.0 6.3 + - + +
136D SER* 1.3 87.6 - - - +
138D LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 3.5 23.6 - - + -
36D ASN* 3.0 28.5 - - + +
37D ASP 3.2 9.0 - - - +
38D SER* 4.7 1.3 - - - -
39D MET* 4.4 1.8 - - + -
49D LEU* 3.6 41.7 - - + -
67D TRP* 4.3 5.2 - - + -
120D GLY 3.4 0.3 - - - +
121D VAL* 3.3 5.2 - - - -
122D TYR* 3.0 54.6 + - + +
137D GLN* 1.3 72.7 - - - +
139D ASN* 1.3 66.1 + - - +
140D LEU* 3.3 3.1 + - + +
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Residues in contact with ASN 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASP 3.5 5.5 + - - -
38D SER* 3.7 13.8 - - - -
39D MET* 2.7 35.5 + - - +
40D TYR* 6.3 0.4 - - + -
120D GLY* 3.6 5.3 - - - +
121D VAL* 3.8 13.7 - - - +
138D LEU* 1.3 70.8 - - - +
140D LEU* 1.3 59.0 + - - +
141D THR* 3.8 11.2 + - - +
1J NAG 1.4 72.1 + - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D MET* 3.2 35.2 - - + +
40D TYR* 4.6 5.6 - - - +
41D GLY 5.2 0.7 - - - +
47D VAL* 4.8 11.9 - - + -
49D LEU* 4.1 16.4 - - + -
111D LEU* 5.2 2.5 - - + -
114D LEU* 3.8 34.5 - - + -
118D ASP* 4.2 16.6 - - + +
119D GLU* 3.2 6.2 - - - +
120D GLY 2.6 43.6 + - - +
122D TYR* 3.8 23.6 - - + -
138D LEU* 3.3 2.5 + - + +
139D ASN* 1.3 73.1 - - - +
141D THR* 1.3 62.5 + - - +
142D VAL* 4.8 4.5 - - + -
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D MET 3.1 6.5 + - - -
40D TYR* 3.4 51.0 - - + +
41D GLY 3.5 3.5 + - - -
119D GLU* 3.7 19.8 + - - +
139D ASN* 4.6 11.8 + - - +
140D LEU* 1.3 76.0 + - - +
142D VAL* 1.3 74.4 + - - +
143D MET* 4.5 4.0 - - + +
178D LYS* 4.0 4.9 - - - +
179D PRO* 6.2 3.6 - - + -
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLY 3.4 12.1 - - - +
43D ILE* 3.8 25.6 - - + -
114D LEU* 4.1 18.4 - - + -
115D GLU 2.9 29.8 - - - +
116D LEU* 3.9 13.5 - - + -
118D ASP* 4.4 2.7 - - + -
119D GLU* 3.4 31.1 - - + +
140D LEU* 4.8 2.0 - - + -
141D THR* 1.3 80.6 - - - +
143D MET* 1.3 63.9 + - - +
144D ALA 4.2 0.4 - - - -
178D LYS* 3.3 25.6 + - - +
179D PRO 5.1 0.2 - - - -
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Residues in contact with MET 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TYR* 4.0 28.0 - - + -
41D GLY 3.1 13.4 + - - +
42D PHE* 3.1 61.0 - - + -
43D ILE* 3.7 4.6 + - - -
141D THR* 4.5 10.5 - - + +
142D VAL* 1.3 79.6 - - - +
144D ALA* 1.3 60.0 + - - +
145D LYS 3.4 0.3 + - - -
178D LYS 3.4 4.3 - - - -
179D PRO* 4.1 20.2 - - + -
230D TYR* 3.6 8.3 - - - +
231D HIS* 4.4 31.4 - - + +
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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