Contacts of the strand formed by residues 34 - 39 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4H LEU* 5.2 6.7 - - - -
27H PHE* 4.9 2.2 - - - -
29H LEU* 3.5 35.4 - - + -
32H TYR* 3.3 15.5 - - + -
33H ARG* 1.3 95.9 - - - +
35H ASN* 1.3 64.1 + - - +
50H SER* 3.2 2.1 - - - -
51H ILE* 2.7 47.1 + - + +
69H ILE* 4.1 0.3 - - - +
71H ARG* 3.6 14.1 - - - +
78H LEU* 3.7 29.6 - - + -
92H CYS* 6.1 0.9 - - - -
93H VAL 3.9 9.6 - - - +
94H ARG* 3.1 40.4 - - + -
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Residues in contact with ASN 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ARG 3.6 9.5 + - - -
34H MET* 1.3 83.5 - - - +
36H TRP* 1.3 66.6 + - - +
47H TRP* 3.1 14.2 + - + +
49H SER 3.1 7.6 - - - +
50H SER* 2.9 24.0 - - - +
69H ILE* 4.9 0.2 - - - -
78H LEU* 3.8 7.2 - - - +
92H CYS* 3.4 4.7 - - - -
93H VAL* 2.9 44.7 + - + +
95H GLU* 2.9 31.3 + - - +
100H PHE* 3.5 17.5 - - - +
96L LEU* 5.5 1.4 - - - +
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Residues in contact with TRP 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 3.7 13.5 - - - -
20H LEU* 3.8 28.7 - - + -
21H SER 4.2 5.4 - - - -
22H CYS* 4.1 10.1 - - + -
35H ASN* 1.3 74.3 - - - +
37H VAL* 1.3 66.1 + - - +
47H TRP* 3.9 1.6 - - - -
48H VAL* 2.9 31.3 + - + -
49H SER* 2.9 13.1 + - - +
69H ILE* 3.6 25.8 - - + +
78H LEU* 3.4 30.3 - - + +
79H TYR* 3.4 20.0 + - - -
80H LEU* 3.5 47.9 - - + +
90H TYR* 4.4 9.6 - - + -
91H TYR 3.3 28.5 - - - -
92H CYS* 3.5 24.2 - - + -
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Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H TRP* 1.3 79.3 - - - +
38H ARG* 1.3 64.0 + - - +
45H LEU* 4.3 5.6 - - + -
46H GLU 3.5 26.7 - - - +
47H TRP* 4.2 7.0 - - + +
48H VAL* 4.2 2.2 - - - -
90H TYR* 3.5 2.5 - - - -
91H TYR* 2.7 43.3 + - - +
93H VAL* 4.0 18.2 - - + -
100H PHE* 4.0 28.7 - - - +
103H TRP* 4.1 26.7 - - + -
98L PHE* 4.2 8.1 - - + -
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Residues in contact with ARG 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 1.3 77.0 - - - +
39H GLN* 1.3 63.2 + - - +
45H LEU* 3.6 1.6 - - - -
46H GLU* 2.9 70.8 + - + +
48H VAL* 3.2 18.3 - - + +
62H SER* 3.7 12.9 + - - -
63H VAL* 3.7 20.5 - - - +
67H PHE* 4.1 1.4 - - - -
85H GLU 4.4 8.1 + - - -
86H ASP* 3.1 33.9 + - - +
88H ALA* 4.2 10.9 - - + +
89H VAL 3.2 8.3 - - - +
90H TYR* 3.1 39.7 + - + -
91H TYR* 5.0 0.9 - - - -
232H GOL 3.8 12.0 + - - -
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Residues in contact with GLN 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 1.3 78.1 - - - +
40H ALA* 1.3 63.0 + - - +
41H PRO 3.9 0.5 - - - -
42H GLY 5.7 0.7 - - - +
43H LYS 3.0 22.7 + - - +
44H GLY 3.5 9.5 + - - +
45H LEU* 3.8 19.5 - - + +
88H ALA* 3.5 2.9 - - - -
89H VAL* 2.7 42.2 + - + +
91H TYR* 3.5 17.6 + - + -
232H GOL 3.4 4.5 - - - -
38L GLN* 2.7 44.0 + - - -
87L TYR* 3.6 8.9 + - - -
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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