Contacts of the strand formed by residues 34 - 41 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N GLN* 3.2 27.3 - - - +
33N PRO* 1.3 86.0 - - + +
35N CYS* 1.3 73.0 + - - +
101N ALA 3.5 10.9 + - - -
102N LEU* 4.1 5.8 - - - +
103N SER* 3.6 0.9 - - - -
201N GLY* 3.8 1.4 - - - -
202N GLY 3.7 3.5 + - - -
372N THR* 4.2 1.3 - - - +
369O LEU* 3.5 31.2 - - - +
370O MET* 3.4 20.3 - - - +
373O GLU* 3.0 33.4 + - + +
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Residues in contact with CYS 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N THR* 1.3 80.2 + - - +
36N THR* 1.3 67.8 + - - +
37N VAL* 4.6 5.4 - - - -
100N LYS* 3.3 3.6 - - - +
101N ALA* 2.7 46.2 + - - +
102N LEU 3.9 3.6 - - - -
103N SER* 3.6 22.9 - - - +
106N MET* 4.8 4.9 - - - -
109N VAL* 6.0 1.6 - - - -
200N ALA 3.1 15.3 - - - +
201N GLY* 3.9 4.0 - - - -
203N ILE* 3.4 28.7 - - + -
372N THR* 3.8 8.0 + - - -
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Residues in contact with THR 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N CYS* 1.3 75.8 + - - +
37N VAL* 1.3 67.0 + - - +
98N TYR* 4.1 19.7 - - + -
99N ILE 3.1 13.9 - - - +
100N LYS* 3.6 5.8 - - + +
199N ALA* 3.3 1.2 - - - -
200N ALA 2.8 35.2 + - - -
372N THR* 2.7 28.8 + - - -
373N THR* 3.2 40.3 + - + +
376N CYS* 3.7 12.4 - - + -
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Residues in contact with VAL 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N CYS* 4.6 4.5 - - - -
36N THR* 1.3 83.2 - - - +
38N GLY* 1.3 54.0 - - - +
98N TYR* 4.2 2.9 - - - -
99N ILE* 2.7 39.3 + - - +
106N MET* 4.8 7.4 - - + +
109N VAL* 3.3 34.3 - - + -
110N VAL* 4.8 4.7 - - + +
113N LEU* 3.8 13.8 - - + +
197N LEU* 5.9 1.8 - - + -
198N ALA 3.1 10.3 - - - +
199N ALA* 3.2 22.0 - - + -
203N ILE* 3.6 22.0 - - + -
208N LEU* 5.1 4.5 - - + -
376N CYS* 4.2 1.8 - - - -
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Residues in contact with GLY 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37N VAL* 1.3 75.8 - - - +
39N VAL* 1.3 60.8 + - - -
40N TRP* 3.5 10.0 - - - -
97N PHE 3.2 13.5 - - - -
98N TYR* 3.6 8.7 - - - -
113N LEU* 3.7 14.5 - - - +
196N VAL 3.6 0.2 - - - +
197N LEU* 3.6 3.4 - - - +
198N ALA 2.9 32.2 + - - +
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Residues in contact with VAL 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N LEU* 5.9 1.3 - - + -
38N GLY* 1.3 74.3 - - - -
40N TRP* 1.3 63.0 + - - +
41N ILE* 3.8 9.8 + - + +
96N ALA* 3.4 3.3 - - - -
97N PHE* 2.8 42.4 + - + +
113N LEU* 5.0 9.6 - - + -
117N VAL* 3.4 29.6 - - + -
195N MET* 3.8 37.7 - - + -
196N VAL 3.2 11.7 - - - +
197N LEU* 4.6 11.2 - - + -
216N PHE* 5.3 6.1 - - + -
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Residues in contact with TRP 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N GLY* 3.5 25.6 - - - -
39N VAL* 1.3 71.7 - - - +
41N ILE* 1.3 61.2 + - - +
89N TYR* 3.5 2.2 + - - -
94N GLN* 3.3 26.0 - - - -
95N THR 3.6 2.2 - - - -
96N ALA* 3.6 15.0 - - + +
98N TYR* 4.0 27.1 - + + -
195N MET* 3.6 1.6 - - - -
196N VAL* 3.0 30.7 + - + +
198N ALA* 3.6 13.2 - - + -
373N THR* 5.0 2.2 - - + -
376N CYS* 3.2 42.0 - - + -
377N GLU* 2.9 50.9 + - + +
380N GLY* 3.5 29.4 - - - +
381N SER* 4.1 1.8 - - - -
384N LEU* 3.6 11.4 - - + +
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Residues in contact with ILE 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N VAL* 4.0 19.3 - - + +
40N TRP* 1.3 76.4 - - - +
42N GLY* 1.3 62.9 + - - +
43N ALA* 2.9 13.2 + - + +
94N GLN* 3.5 4.5 - - - -
95N THR* 2.7 44.0 + - - +
97N PHE* 4.3 18.2 - - + -
117N VAL* 4.7 4.5 - - + -
189N HIS 4.3 8.7 - - - +
190N PHE* 3.3 48.0 - - + -
194N ARG* 3.6 11.4 - - + +
195N MET* 4.0 17.9 - - + -
384N LEU* 3.5 6.6 - - - +
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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