Contacts of the strand formed by residues 34 - 40 (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 TYR 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C PRO* 3.5 1.6 - - - +
28C ASP* 2.8 48.3 + - + -
31C ASN* 3.1 26.7 + - + +
32C ALA 3.3 0.4 - - - -
33C ARG* 1.3 78.8 - - - +
35C PHE* 1.3 69.8 + - - +
36C HIS* 3.7 17.7 - + - -
55C GLU* 2.6 41.0 + - + -
56C LEU 3.5 9.2 - - - -
57C PHE* 4.6 0.9 - - - -
59I ASN* 3.6 32.1 - - - +
63I ALA 4.9 0.2 + - - -
66I LEU* 3.9 20.5 - - + +
67I SER* 3.2 23.7 + - - -
70I THR* 4.0 7.7 + - - -
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Residues in contact with PHE 35 (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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12C THR* 3.9 21.1 - - + -
15C LEU* 3.6 28.3 - - + -
26C GLU 3.3 7.2 - - - +
27C PRO* 3.6 36.1 - - + -
32C ALA 3.6 22.7 - - - -
33C ARG 3.7 8.5 - - - -
34C TYR* 1.3 76.8 - - - +
36C HIS* 1.3 65.1 + - - +
37C VAL* 4.5 8.5 - - + -
54C LEU 4.1 0.2 - - - +
55C GLU* 3.6 5.4 - - - -
56C LEU* 2.7 60.3 + - + +
58C LEU* 3.6 29.6 - - + -
101C ILE* 4.2 7.4 - - + -
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Residues in contact with HIS 36 (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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24C LYS 3.8 0.7 - - - +
25C ALA* 3.4 2.4 - - - -
26C GLU* 2.7 46.8 + - + +
27C PRO 4.7 1.6 - - - -
28C ASP* 2.8 46.9 + - + +
34C TYR* 3.7 19.1 - + - -
35C PHE* 1.3 72.5 - - - +
37C VAL* 1.3 61.0 + - - +
38C VAL* 5.5 2.2 - - + +
54C LEU 3.9 2.5 - - - -
55C GLU* 2.6 36.0 + - - +
70I THR* 4.0 14.6 - - + +
74I GLU* 6.1 1.3 - - - -
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Residues in contact with VAL 37 (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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15C LEU* 6.3 0.2 - - + -
23C ILE* 4.4 1.8 - - + -
24C LYS 3.2 8.5 - - - +
25C ALA* 4.0 15.5 - - + -
35C PHE* 4.4 12.8 - - + +
36C HIS* 1.3 83.2 - - - +
38C VAL* 1.3 65.6 + - - +
39C ILE* 4.0 20.0 - - + -
53C LYS* 3.3 5.7 - - - +
54C LEU* 2.7 49.2 + - + +
56C LEU* 4.6 9.9 - - + -
69C VAL* 6.4 0.2 - - + -
101C ILE* 5.9 0.2 - - + -
105C LEU* 3.9 37.7 - - + -
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Residues in contact with VAL 38 (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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22C GLY 3.8 0.9 - - - +
23C ILE* 3.5 2.8 - - - -
24C LYS* 2.8 47.0 + - + +
36C HIS 5.5 1.6 - - - -
37C VAL* 1.3 79.5 - - - +
39C ILE* 1.3 66.3 + - - +
40C ALA 4.2 0.9 - - - +
51C THR* 3.9 30.3 - - + +
52C PHE 3.3 8.5 - - - +
53C LYS* 4.9 7.6 - - + -
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Residues in contact with ILE 39 (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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22C GLY 3.3 8.7 - - - +
23C ILE* 4.4 10.3 - - + -
37C VAL* 4.0 12.3 - - + -
38C VAL* 1.3 78.8 - - - +
40C ALA* 1.3 73.5 + - - +
52C PHE* 2.9 37.9 + - + +
54C LEU* 3.8 23.6 - - + -
71C PHE* 5.6 0.7 - - + -
105C LEU* 4.1 19.3 - - - +
108C ILE* 3.8 29.4 - - + -
109C GLN* 4.3 19.5 - - + +
112C LEU* 4.3 15.5 - - + -
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Residues in contact with ALA 40 (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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22C GLY* 2.9 27.1 + - - +
38C VAL* 4.2 1.8 - - - +
39C ILE* 1.3 84.0 - - - +
41C GLY* 1.3 68.9 - - - +
42C PRO* 3.1 9.8 - - + +
50C GLY 3.7 6.7 - - - +
51C THR* 4.6 10.1 - - + +
52C PHE* 4.6 0.2 - - - -
109C GLN* 4.9 3.8 + - - -
112C LEU* 4.6 0.4 - - - +
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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