Contacts of the strand formed by residues 41 - 47 (chain L) in PDB entry 2ZHX
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 ILE 41 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L ILE 3.5 1.2 - - - +
23L LEU* 3.1 8.7 - - - +
24L MET* 2.8 38.4 + - - +
25L LEU 5.3 0.2 - - - -
29L VAL* 4.2 17.5 - - + -
37L PRO* 3.7 19.5 - - + -
39L SER 4.2 5.6 - - - +
40L ASP* 1.3 80.0 - - - +
42L LEU* 1.3 74.2 + - - +
43L VAL* 3.9 3.1 + - + +
58L LEU* 3.8 21.8 - - + -
59L THR 3.4 13.9 - - - +
60L SER* 5.0 1.8 - - - -
68L TRP* 3.3 48.7 - - + -
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Residues in contact with LEU 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K PRO 4.8 1.6 - - - +
138K ALA* 4.3 14.8 - - + -
141K ARG* 4.5 10.3 - - - +
21L SER* 3.9 16.4 - - - +
22L ILE 3.3 3.1 - - - -
23L LEU* 3.7 39.7 - - + +
41L ILE* 1.3 73.0 - - - +
43L VAL* 1.3 59.8 + - - +
44L HIS* 3.0 44.6 + - + +
57L LEU 3.3 1.6 - - - +
58L LEU* 3.3 1.6 - - - -
59L THR 3.0 22.5 + - - +
60L SER 4.0 16.1 + - - +
61L ASP* 4.1 14.1 - - - -
62L ALA 4.3 2.7 - - - +
65L TYR* 4.2 13.0 - - + -
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Residues in contact with VAL 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193K SER* 4.1 4.3 - - - +
195K LEU* 3.7 45.1 - - + -
20L GLU 4.4 0.2 - - - -
21L SER* 3.8 1.2 - - - -
22L ILE* 2.6 40.4 + - + +
24L MET* 3.7 22.0 - - + -
29L VAL* 5.6 0.4 - - + -
41L ILE* 4.4 11.9 - - + +
42L LEU* 1.3 68.9 - - - +
44L HIS* 1.3 57.0 + - - +
45L THR* 3.0 26.0 + - - +
56L MET* 4.3 15.0 - - + -
57L LEU 3.8 2.2 - - - -
58L LEU* 4.5 7.0 - - + -
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Residues in contact with HIS 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137K PRO* 4.1 13.6 - - + +
4L LEU* 4.3 15.3 - - + +
8L ILE* 4.9 2.9 - - - +
18L ILE* 4.3 26.9 - - + -
20L GLU 3.5 6.3 - - - +
21L SER* 3.0 27.9 + - - +
42L LEU* 3.0 40.6 + - + +
43L VAL* 1.3 67.0 - - - +
45L THR* 1.3 59.7 + - - +
55L VAL 3.7 1.9 - - - +
56L MET* 3.3 3.7 - - - -
57L LEU* 2.7 52.3 + - + +
59L THR* 3.0 38.0 - - + +
65L TYR* 4.7 2.9 - + - -
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Residues in contact with THR 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K ARG* 4.3 11.9 - - + +
193K SER* 3.8 4.0 + - - -
194K PRO* 3.9 26.9 - - + -
18L ILE* 4.0 0.4 - - - -
19L GLN* 3.1 23.0 + - - +
20L GLU* 2.9 37.1 + - + +
43L VAL* 3.0 18.9 + - - +
44L HIS* 1.3 72.3 - - - +
46L ALA* 1.3 67.7 + - - +
54L ASN* 4.7 4.3 - - + -
55L VAL 3.6 2.7 - - - +
56L MET* 3.7 24.2 - - + +
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Residues in contact with ALA 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L ILE* 5.2 7.0 - - + -
16L LEU* 4.3 14.8 - - + -
17L VAL 3.2 30.7 - - - +
18L ILE* 3.8 10.3 - - + -
19L GLN* 4.4 3.6 - - - +
44L HIS 5.3 0.2 - - - +
45L THR* 1.3 77.9 - - - +
47L TYR* 1.3 61.5 + - - +
54L ASN* 3.9 1.4 - - - -
55L VAL* 2.9 41.3 + - + +
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Residues in contact with TYR 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K PRO* 4.6 12.3 - - + -
92K ARG* 3.1 48.6 + - + +
16L LEU* 4.3 13.8 - - - +
17L VAL 4.4 3.2 + - - +
19L GLN* 3.9 24.7 + - - +
46L ALA* 1.3 75.6 - - - +
48L ASP* 1.3 72.7 + - - +
49L GLU* 3.7 29.7 + - + +
52L ASP* 2.9 35.6 + - - +
53L GLU 3.9 12.3 - - - -
54L ASN* 3.3 18.6 - - - -
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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