Contacts of the strand formed by residues 44 - 51 (chain H) in PDB entry 43C9
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 GLY 44 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87G PHE* 6.2 2.5 - - - -
38H ARG 3.6 1.2 - - - +
39H GLN* 3.4 9.1 - - - -
40H SER* 3.1 36.7 + - - -
41H PRO 4.4 2.1 + - - -
42H GLY 3.4 2.8 + - - -
43H LYS* 1.3 80.6 - - - +
45H LEU* 1.3 62.4 + - - -
46H GLU* 3.7 3.8 + - - +
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G TYR* 6.5 0.2 - - + -
44G PRO* 4.5 9.0 - - + -
87G PHE* 3.6 46.8 - - + -
98G PHE* 3.5 48.0 + - + +
99G GLY 5.6 1.0 + - - +
37H VAL* 3.5 27.4 - - + -
38H ARG 3.6 0.7 - - - -
39H GLN* 3.8 33.6 - - + +
43H LYS 4.3 2.1 - - - +
44H GLY* 1.3 72.3 - - - -
46H GLU* 1.3 64.1 + - - +
91H TYR* 5.8 0.7 - - + -
103H TRP* 4.2 11.9 - - + -
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G PHE* 4.0 4.6 - - - -
37H VAL* 3.4 3.8 - - - +
38H ARG* 3.0 80.2 + - + +
40H SER* 4.5 0.5 + - - -
43H LYS* 3.1 42.8 - - - +
44H GLY 4.1 3.3 - - - +
45H LEU* 1.3 79.8 - - - +
47H TRP* 1.3 64.5 + - - +
48H LEU* 3.7 5.2 + - + +
60H ASN* 5.6 2.7 - - - +
63H LEU* 5.7 2.4 - - + +
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Residues in contact with TRP 47 (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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89G GLN* 3.8 15.0 - - - -
94G ALA* 3.9 9.0 - - + -
95G PRO* 3.2 42.4 - - + -
96G ARG* 3.3 35.8 - - + +
97G THR* 4.7 1.9 - - - +
98G PHE* 3.7 9.7 - - + -
35H HIS* 2.9 33.7 + + + -
36H TRP 4.0 1.6 - - - -
37H VAL* 4.3 12.3 - - + -
46H GLU* 1.3 72.2 - - - +
48H LEU* 1.3 63.5 + - - +
49H GLY* 3.4 36.4 + - - -
50H MET* 3.6 20.6 - - + -
58H GLU* 3.9 26.0 - - + -
59H TYR 4.1 11.0 - - - -
60H ASN* 2.8 29.9 + - - +
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Residues in contact with LEU 48 (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* 2.7 35.7 + - + +
37H VAL* 4.4 5.4 - - - +
38H ARG* 4.1 22.4 - - + +
46H GLU* 4.3 8.3 - - + +
47H TRP* 1.3 79.0 - - - +
49H GLY* 1.3 55.3 + - - +
59H TYR* 3.7 0.5 - - - -
60H ASN* 2.8 27.5 + - - +
63H LEU* 3.6 27.1 - - + -
67H LEU* 3.5 23.0 - - + +
69H ILE* 4.8 2.0 - - + -
80H LEU* 3.6 31.2 - - + -
82H MET* 6.0 1.3 - - - -
90H TYR* 3.8 20.9 - - + -
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Residues in contact with GLY 49 (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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35H HIS* 3.5 1.6 - - - -
36H TRP 3.0 21.1 + - - -
47H TRP* 3.4 22.8 - - - -
48H LEU* 1.3 81.0 - - - +
50H MET* 1.3 63.5 + - - +
58H GLU 3.2 14.1 - - - -
59H TYR* 4.0 0.4 - - - -
69H ILE* 3.8 13.2 - - - +
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Residues in contact with MET 50 (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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96G ARG* 3.6 33.0 - - - +
33H ASN* 4.3 11.0 - - + -
34H VAL 3.2 13.5 - - - +
35H HIS* 3.0 33.9 - - + +
36H TRP* 5.7 0.2 - - - -
47H TRP* 3.6 13.0 - - + -
49H GLY* 1.3 74.9 - - - +
51H ILE* 1.3 62.4 + - - +
52H TRP* 3.7 44.0 - - + +
57H ILE* 3.5 10.0 - - - +
58H GLU* 3.0 43.6 + - + +
69H ILE* 3.8 8.0 - - - +
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Residues in contact with ILE 51 (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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32H TYR 4.2 1.4 - - - +
33H ASN* 3.6 1.8 - - - -
34H VAL* 2.8 41.7 + - + +
50H MET* 1.3 76.0 - - - +
52H TRP* 1.3 71.1 + - - +
55H GLY* 4.2 7.9 - - - -
56H SER 3.3 10.8 - - - +
57H ILE* 4.0 18.8 - - + -
69H ILE* 4.1 7.4 - - + -
70H SER* 3.8 18.8 - - - -
71H LYS* 3.5 43.4 + - + +
78H ILE* 3.9 23.8 - - + -
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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