Contacts of the strand formed by residues 18 - 24 (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 18 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71K PRO* 4.0 9.7 - - + +
72K THR* 3.4 19.8 - - - +
137K PRO* 5.5 2.0 - - + -
4L LEU* 4.0 31.2 - - + -
5L SER* 4.1 24.9 - - - +
8L ILE* 4.3 17.3 - - + -
17L VAL* 1.3 75.9 - - - +
19L GLN* 1.3 62.6 + - - +
20L GLU 3.5 21.5 - - - +
21L SER* 3.8 12.8 - - - +
44L HIS* 4.3 18.4 - - + -
45L THR 4.2 2.0 - - - +
46L ALA* 3.8 10.1 - - + -
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Residues in contact with GLN 19 (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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70K TYR* 3.5 14.1 - - - +
71K PRO* 3.2 19.3 - - - +
72K THR* 3.8 11.3 - - + +
75K HIS* 4.7 11.8 - - + -
89K PRO* 2.7 41.2 + - - +
90K TRP 3.6 5.1 - - - +
91K PRO* 3.3 34.9 - - + +
92K ARG* 3.6 6.6 + - - +
17L VAL* 3.4 16.6 - - + +
18L ILE* 1.3 75.0 - - - +
20L GLU* 1.3 62.4 + - + +
45L THR 3.1 8.7 + - - +
46L ALA* 4.5 2.3 - - - -
47L TYR* 3.9 23.4 + - - +
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Residues in contact with GLU 20 (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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70K TYR* 4.3 15.2 - - + -
71K PRO* 4.3 5.4 - - - -
91K PRO* 3.9 4.5 - - + +
92K ARG 3.7 5.9 + - - +
93K SER* 2.6 55.3 + - - -
193K SER* 3.8 4.9 + - - -
18L ILE* 3.5 3.7 - - - +
19L GLN* 1.3 83.0 - - + +
21L SER* 1.3 68.3 + - - +
22L ILE* 3.1 23.6 - - + +
44L HIS* 3.5 1.2 - - - -
45L THR* 2.9 54.6 + - - +
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Residues in contact with SER 21 (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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67K GLN* 3.7 8.5 - - - +
68K ASP* 4.2 12.0 - - - +
71K PRO* 4.6 3.7 - - - +
137K PRO* 3.3 33.0 - - - +
18L ILE* 3.8 6.1 - - - +
20L GLU* 1.3 78.3 + - - +
22L ILE* 1.3 65.7 + - - +
42L LEU* 3.9 12.1 - - - +
43L VAL 3.8 4.7 - - - -
44L HIS* 3.0 33.0 - - - +
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Residues in contact with ILE 22 (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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67K GLN* 3.6 15.7 - - + +
70K TYR* 6.2 1.8 - - + -
81K PHE* 5.8 2.0 - - + -
93K SER* 4.4 1.6 - - - +
191K HIS* 3.5 51.4 - - + +
193K SER* 4.3 5.4 - - - -
20L GLU* 3.1 34.5 - - + +
21L SER* 1.3 81.7 - - - +
23L LEU* 1.3 65.8 + - - +
24L MET* 4.1 9.6 - - + -
42L LEU* 3.3 2.5 - - - -
43L VAL* 2.6 50.0 + - + +
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Residues in contact with LEU 23 (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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67K GLN* 2.7 37.6 + - - +
141K ARG* 3.9 20.0 - - - +
169K GLY* 5.9 1.4 - - - -
170K ARG 5.6 0.3 + - - -
171K ASP* 3.7 30.7 + - + +
22L ILE* 1.3 70.4 - - - +
24L MET* 1.3 72.3 + - - +
25L LEU* 5.3 4.9 - - + -
28L GLU* 4.5 1.0 - - - +
40L ASP* 3.8 28.7 - - + +
41L ILE* 3.1 30.1 - - - +
42L LEU* 3.7 19.9 - - + +
61L ASP* 4.1 17.0 - - - +
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Residues in contact with MET 24 (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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169K GLY* 5.2 1.1 - - - -
171K ASP 5.7 0.4 - - - +
190K PRO* 5.5 0.7 - - + -
191K HIS* 4.2 11.0 - - + +
193K SER* 5.1 3.1 - - - -
195K LEU* 4.2 15.0 - - - -
196K SER* 3.6 32.8 - - - +
22L ILE* 4.1 12.3 - - + -
23L LEU* 1.3 82.1 - - - +
25L LEU* 1.3 70.4 + - - +
28L GLU* 3.2 52.7 - - + +
29L VAL* 4.4 8.5 - - + -
32L VAL* 6.5 0.4 - - + -
40L ASP* 3.8 2.8 - - - +
41L ILE* 2.8 34.1 + - - +
43L VAL* 3.7 26.0 - - + -
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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