Contacts of the strand formed by residues 34 - 39 (chain M) in PDB entry 3INU
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 MET 34 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4M LEU* 4.9 6.7 - - - -
27M PHE* 4.9 2.0 - - + -
29M LEU* 3.8 37.9 - - + -
32M TYR* 3.3 12.8 - - + +
33M ARG* 1.3 99.0 - - - +
35M ASN* 1.3 66.8 + - - +
50M SER* 3.3 0.3 - - - -
51M ILE* 2.9 34.3 + - + +
71M ARG* 3.4 18.6 - - - +
78M LEU* 3.7 28.9 - - + -
92M CYS* 6.5 0.2 - - - -
93M VAL 4.1 2.9 - - - +
94M ARG* 3.0 45.5 - - + -
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Residues in contact with ASN 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M ARG 3.5 10.1 + - - -
34M MET* 1.3 84.1 + - - +
36M TRP* 1.3 71.5 + - - +
47M TRP* 3.1 16.6 + - + +
49M SER 3.1 7.0 - - - +
50M SER* 2.9 23.0 - - - +
78M LEU* 3.9 1.2 - - - +
92M CYS* 3.4 7.3 - - - +
93M VAL* 2.8 42.3 + - + +
95M GLU* 3.2 30.7 + - - +
100M PHE* 3.7 20.4 - - - +
96N LEU* 4.8 1.4 - - - +
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Residues in contact with TRP 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M GLU* 3.7 13.0 - - - -
20M LEU* 3.8 29.4 - - + -
21M SER 4.2 14.6 - - - -
22M CYS* 4.2 0.7 - - + -
35M ASN* 1.3 76.2 - - - +
37M VAL* 1.3 67.6 + - - +
47M TRP* 3.7 2.4 - - - -
48M VAL* 2.9 33.3 + - + -
49M SER* 2.8 12.3 + - - +
69M ILE* 3.6 24.7 - - + +
78M LEU* 3.5 32.8 - - + +
79M TYR 3.4 19.2 + - - -
80M LEU* 3.5 43.7 - - + +
90M TYR* 4.4 9.4 - - + -
91M TYR 3.2 23.6 - - - -
92M CYS* 3.6 21.3 - - + -
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Residues in contact with VAL 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M ASN* 5.1 0.2 - - + -
36M TRP* 1.3 81.0 - - - +
38M ARG* 1.3 68.5 + - - +
45M LEU* 4.3 13.5 - - + -
46M GLU 3.5 19.5 - - - +
47M TRP* 4.3 8.5 - - + -
48M VAL* 4.4 1.1 - - - +
90M TYR* 3.5 2.1 - - - +
91M TYR* 2.6 40.8 + - + +
93M VAL* 3.6 24.0 - - + -
100M PHE* 4.0 27.4 - - - +
103M TRP* 3.9 22.7 - - + -
98N PHE* 4.4 3.4 - - + -
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Residues in contact with ARG 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M VAL* 1.3 78.6 - - - +
39M GLN* 1.3 63.1 + - - +
44M GLY 4.0 0.3 - - - +
45M LEU* 3.7 1.6 - - - -
46M GLU* 2.7 70.7 + - - +
48M VAL* 3.7 11.9 - - + +
62M SER* 4.0 18.2 + - - -
63M VAL* 3.8 19.7 - - - +
66M ARG* 5.3 0.4 - - - +
67M PHE* 4.0 0.8 - - - -
85M GLU* 4.3 12.6 + - - +
86M ASP* 3.1 26.9 + - - +
88M ALA* 4.2 6.1 - - + -
89M VAL 3.1 9.9 - - - +
90M TYR* 3.1 46.4 + - + -
91M TYR* 5.0 0.7 - - - -
232M GOL 3.7 14.1 + - - +
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Residues in contact with GLN 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M ARG* 1.3 76.3 - - - +
40M ALA* 1.3 69.7 + - - +
41M PRO* 3.6 0.7 - - - +
42M GLY 5.8 0.2 - - - +
43M LYS 2.9 22.4 + - - +
44M GLY 3.1 17.4 + - - +
45M LEU* 3.7 18.6 - - + +
88M ALA* 3.6 2.9 - - - -
89M VAL* 2.8 36.7 + - + +
91M TYR* 3.7 18.3 + - + -
232M GOL 3.8 0.7 - - - -
38N GLN* 3.0 41.6 + - - -
87N TYR* 3.4 9.3 + - - -
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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