Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 3L73
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 THR 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.2 25.2 - - + +
33A PRO* 1.3 86.2 - - + +
35A CYS* 1.3 73.8 + - - +
101A ALA 3.4 12.7 + - - -
102A LEU* 4.2 4.9 - - - +
103A SER* 3.6 0.9 - - - +
201A GLY* 3.8 1.7 - - - -
202A GLY 3.7 3.6 + - - -
372A THR* 4.2 1.3 - - - +
369B LEU* 3.4 32.5 - - - +
370B MET* 3.5 17.9 - - - +
373B GLU* 2.9 33.6 + - + +
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Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 1.3 79.3 + - - +
36A THR* 1.3 69.6 + - - +
37A VAL* 4.5 5.4 - - - -
100A LYS* 3.4 3.5 - - - +
101A ALA* 2.7 46.1 + - - -
102A LEU 4.0 4.0 - - - -
103A SER* 3.8 20.2 - - - +
106A MET* 4.9 4.9 - - - -
109A VAL* 5.9 1.6 - - - -
200A ALA 3.2 15.7 - - - +
201A GLY* 3.9 3.8 - - - -
203A ILE* 3.6 28.5 - - + -
372A THR* 3.8 7.5 + - - -
373B GLU* 4.8 0.3 - - - +
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 1.3 76.3 + - - +
37A VAL* 1.3 69.1 + - - +
98A TYR* 4.1 15.3 - - + -
99A ILE 3.1 17.3 - - - +
100A LYS* 3.7 7.1 - - + +
199A ALA* 3.3 1.0 - - - -
200A ALA 2.8 35.7 + - - -
372A THR* 2.7 30.1 + - - -
373A THR* 3.2 38.0 + - + +
376A CYS* 3.7 10.6 - - + -
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Residues in contact with VAL 37 (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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35A CYS* 4.5 3.6 - - - -
36A THR* 1.3 83.2 - - - +
38A GLY* 1.3 55.3 - - - +
98A TYR* 4.1 2.7 - - - -
99A ILE* 2.7 37.3 + - - +
106A MET* 4.8 5.2 - - + +
109A VAL* 3.4 33.4 - - + -
110A VAL* 4.7 8.5 - - + -
113A LEU* 3.8 13.6 - - + +
197A LEU* 5.9 1.8 - - + -
198A ALA 3.2 9.9 - - - +
199A ALA* 3.2 22.4 - - + -
203A ILE* 3.6 21.5 - - + -
208A LEU* 5.1 4.9 - - + -
376A CYS* 4.2 1.1 - - - -
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Residues in contact with GLY 38 (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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37A VAL* 1.3 75.8 - - - +
39A VAL* 1.3 61.2 + - - -
40A TRP* 3.5 11.3 - - - -
97A PHE 3.2 12.8 - - - -
98A TYR* 3.6 8.7 - - - -
113A LEU* 3.7 13.9 - - - +
197A LEU* 3.5 3.9 - - - +
198A ALA 2.8 32.3 + - - +
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Residues in contact with VAL 39 (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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23A LEU* 6.0 2.0 - - + -
38A GLY* 1.3 72.7 - - - -
40A TRP* 1.3 64.5 + - - +
41A ILE* 3.7 12.5 + - + +
96A ALA* 3.4 3.6 - - - -
97A PHE* 2.9 36.5 + - + +
113A LEU* 5.0 9.4 - - + -
117A VAL* 3.4 30.3 - - + -
195A MET* 3.9 33.2 - - + -
196A VAL 3.2 13.2 - - - +
197A LEU* 4.6 11.0 - - + -
216A PHE* 5.4 4.9 - - + -
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Residues in contact with TRP 40 (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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36A THR* 5.4 0.2 - - + -
38A GLY* 3.5 26.2 - - - -
39A VAL* 1.3 71.9 - - - +
41A ILE* 1.3 61.2 + - - +
89A TYR* 3.5 2.8 + - - -
94A GLN* 3.3 26.0 - - - -
95A THR 3.6 2.5 - - - -
96A ALA* 3.7 14.5 - - + +
98A TYR* 4.0 27.6 - + + -
195A MET* 3.7 1.2 - - - -
196A VAL* 3.0 30.4 + - + +
198A ALA* 3.6 13.5 - - + -
373A THR* 5.1 2.0 - - + -
376A CYS* 3.2 39.9 - - + -
377A GLU* 3.0 49.9 + - + -
380A GLY* 3.6 30.5 - - - +
381A SER* 4.2 0.4 - - - -
384A LEU* 3.5 11.9 - - + +
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Residues in contact with ILE 41 (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 VAL* 3.9 20.6 - - + +
40A TRP* 1.3 76.2 - - - +
42A GLY* 1.3 62.7 + - - +
43A ALA* 3.0 14.6 + - + +
94A GLN* 3.5 4.7 - - - -
95A THR* 2.8 41.6 + - - +
97A PHE* 4.3 17.7 - - + -
117A VAL* 4.6 4.7 - - + -
189A HIS 4.3 8.3 - - - +
190A PHE* 3.2 47.1 - - + -
194A ARG* 3.7 10.8 - - + +
195A MET* 4.1 18.8 - - + -
384A LEU* 3.6 6.5 - - - +
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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