Contacts of the strand formed by residues 45 - 51 (chain I) in PDB entry 3SKJ
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 LEU 45 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37I VAL* 4.2 9.0 - - + -
38I ARG 3.3 7.9 - - - +
39I GLN* 3.8 33.7 - - + +
44I GLY* 1.3 75.9 - - - -
46I GLU* 1.3 61.0 + - - +
91I TYR* 4.2 15.3 - - + -
103I TRP* 4.6 10.5 - - + -
36M TYR* 5.8 1.3 - - + -
38M GLN* 5.1 0.9 - - - +
44M PRO* 4.9 9.0 - - + -
87M TYR* 3.6 37.0 - - + -
98M PHE* 3.5 60.0 + - + +
99M GLY 4.9 0.8 + - - -
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Residues in contact with GLU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I VAL* 3.8 2.9 - - - -
38I ARG* 2.7 71.9 + - + +
44I GLY 5.0 2.0 - - - +
45I LEU* 1.3 78.1 - - - +
47I TRP* 1.3 72.7 + - - +
48I VAL* 3.7 4.7 + - - +
60I ALA* 4.7 5.2 - - + +
62I SER* 3.1 24.8 + - - -
98M PHE* 4.5 1.6 - - - -
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Residues in contact with TRP 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ALA* 4.3 0.6 - - + +
36I TRP 3.9 7.6 - - - -
37I VAL* 4.0 12.4 - - + +
46I GLU* 1.3 82.5 - - - +
48I VAL* 1.3 61.6 + - - +
49I SER* 3.2 32.6 + - - -
50I ARG* 3.7 14.3 - - + +
58I HIS* 3.8 6.7 - - + -
59I TYR 3.7 24.9 - - - -
60I ALA* 3.4 40.4 - - + +
100I PHE* 3.4 38.2 - + + +
94M TYR* 4.2 13.7 - + - -
95M SER 5.0 4.8 + - - +
96M ARG* 3.2 61.2 + - + +
98M PHE* 4.2 10.6 - - + -
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Residues in contact with VAL 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TRP* 2.9 20.0 + - + +
37I VAL 4.6 0.4 - - - -
38I ARG* 3.6 44.9 - - + +
46I GLU* 3.8 6.7 - - - +
47I TRP* 1.3 82.2 - - - +
49I SER* 1.3 64.2 + - - +
59I TYR* 3.3 3.8 - - - +
60I ALA* 2.7 33.6 + - + +
63I VAL* 4.1 9.7 - - + +
67I PHE* 3.7 31.0 - - + -
80I LEU* 4.4 11.0 - - + -
90I TYR* 4.5 3.1 - - + -
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Residues in contact with SER 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I ALA* 3.3 1.2 - - - -
36I TRP* 3.0 24.7 + - - -
47I TRP* 3.2 14.8 + - - -
48I VAL* 1.3 88.8 - - - +
50I ARG* 1.3 61.8 + - - +
58I HIS 2.7 20.0 + - - -
59I TYR* 3.0 28.0 - - - -
69I ILE* 3.1 24.0 - - - +
80I LEU* 4.3 7.2 - - - -
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Residues in contact with ARG 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLU 5.8 1.4 + - - -
135F ARG* 6.1 2.8 - - - +
33I MET* 3.5 21.8 - - - +
34I MET 3.4 11.9 - - - +
35I ALA* 4.2 2.5 - - + -
47I TRP* 3.7 22.4 - - + +
49I SER* 1.3 75.0 + - - +
51I ILE* 1.3 66.7 + - - +
52I GLY* 4.7 0.8 - - - +
56I PRO* 4.6 8.9 + - - +
57I THR* 3.4 9.5 + - - -
58I HIS* 2.9 55.1 + - + +
69I ILE* 3.7 4.6 - - - +
100I GLU* 2.9 62.2 + - + +
96M ARG* 3.6 11.2 - - - +
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Residues in contact with ILE 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I MET* 3.4 4.5 - - - +
34I MET* 2.9 36.0 + - + +
50I ARG* 1.3 76.2 - - - +
52I GLY* 1.3 66.8 + - - +
54I GLY* 3.4 26.2 - - - +
56I PRO 3.7 4.9 - - - +
57I THR* 4.9 3.8 - - - +
69I ILE* 3.8 16.6 - - + +
70I SER* 3.5 35.0 - - - +
71I ARG* 3.3 25.5 + - + +
78I LEU* 3.9 22.9 - - + -
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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