Contacts of the strand formed by residues 51 - 57 (chain C) in PDB entry 4DHJ
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 51 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.9 21.4 - - + +
39C ILE 3.8 3.4 - - - -
40C ALA* 4.8 9.4 - - + -
49C GLY 4.8 2.9 - - - +
50C GLY* 1.3 79.5 - - - +
52C PHE* 1.3 62.7 + - - +
53C LYS 4.1 0.2 - - - -
73C THR* 3.9 0.5 - - - +
148C ALA* 3.0 14.3 + - - +
150C ASN* 2.6 33.3 + - - +
241I ASN* 3.0 28.3 + - - +
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Residues in contact with PHE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.3 5.4 - - - -
39C ILE* 2.9 48.8 + - + +
41C GLY* 3.9 9.9 - - - -
47C PHE* 3.8 44.6 - + + -
50C GLY 3.9 8.5 - - - -
51C THR* 1.3 74.1 - - - +
53C LYS* 1.3 63.6 + - - +
54C LEU* 3.5 6.3 - - + +
71C PHE* 3.8 22.0 - + + -
73C THR* 3.5 19.5 - - + -
74C LYS 4.2 2.2 - - - -
75C ILE* 3.6 36.8 - - + -
112C LEU* 4.4 7.9 - - + -
144C THR* 4.2 7.4 - - - -
148C ALA* 3.6 22.0 - - + -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL 3.3 7.9 - - - +
38C VAL* 4.5 8.3 - - + +
51C THR 4.1 0.8 - - - -
52C PHE* 1.3 71.7 - - - +
54C LEU* 1.3 63.0 + - - +
55C GLU* 5.9 0.7 - - - +
71C PHE* 3.7 4.2 - - - -
72C MET* 2.9 63.5 + - + +
73C THR* 2.7 40.8 + - - +
68I LYS* 5.1 1.2 - - - +
71I GLU* 2.8 38.3 + - - +
239I ALA* 4.0 5.7 + - - +
240I PRO 3.6 13.9 + - - -
241I ASN* 3.3 33.2 + - - +
242I GLY 3.5 0.2 - - - +
243I GLY* 4.2 1.8 - - - +
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 2.7 45.5 + - + +
39C ILE* 3.8 26.2 - - + -
52C PHE 3.5 17.3 - - - +
53C LYS* 1.3 77.2 - - - +
55C GLU* 1.3 70.6 + - - +
69C VAL* 3.8 26.2 - - + -
70C ARG 3.3 9.2 - - - +
71C PHE* 3.9 29.8 - - + -
72C MET 4.2 0.4 - - - +
86C ILE* 4.3 2.0 - - + -
105C LEU* 4.9 4.3 - - + -
108C ILE* 3.8 26.9 - - + -
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Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C TYR* 2.6 26.8 + - + -
35C PHE 3.6 1.6 - - - -
36C HIS* 2.6 32.2 + - - +
53C LYS* 5.9 1.0 - - - +
54C LEU* 1.3 82.0 - - - +
56C LEU* 1.3 61.5 + - - +
68C LYS 3.6 0.9 - - - +
69C VAL* 3.2 6.8 - - - +
70C ARG* 2.8 43.5 + - - +
72C MET* 3.4 32.9 - - + +
67I SER* 2.6 35.4 + - - +
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG 3.7 0.7 - - - +
34C TYR* 3.5 7.2 - - - -
35C PHE* 2.7 68.5 + - + +
37C VAL* 4.6 7.6 - - + -
55C GLU* 1.3 76.0 - - - +
57C PHE* 1.3 64.2 + - - +
58C LEU* 3.7 24.7 - - + -
67C PRO* 4.2 7.2 - - + -
68C LYS 3.1 8.7 - - - +
69C VAL* 3.8 21.3 - - + -
101C ILE* 3.8 34.3 - - + -
104C VAL* 5.2 1.6 - - + -
105C LEU* 4.2 15.9 - - + -
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ASN* 4.6 8.5 - - - -
33C ARG* 3.4 29.2 - - + -
34C TYR* 4.6 0.2 - - - -
56C LEU* 1.3 74.6 - - - +
58C LEU* 1.3 79.3 + - - +
59C PRO* 3.3 24.1 - - + +
60C GLU 5.1 1.6 - - - -
67C PRO* 3.5 3.1 - - - +
68C LYS* 2.7 64.9 + - + +
59I ASN* 3.5 52.0 - - + +
60I GLU* 3.7 27.6 - - + -
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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