Contacts of the strand formed by residues 31 - 36 (chain X) in PDB entry 1ZEQ
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 LYS 31 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X GLY 4.8 0.3 - - - -
25X ILE* 3.8 0.3 - - - -
26X ASP* 2.8 41.7 + - + +
29X SER* 3.4 22.7 - - - +
30X LYS* 1.3 91.1 - - - +
32X ILE* 1.3 64.3 + - - +
33X THR* 4.1 3.0 + - - +
50X ARG* 4.6 24.7 - - + -
51X PHE 3.2 11.2 - - - +
52X THR* 2.7 28.9 + - - +
53X ILE* 4.2 0.2 - - - +
78X LEU* 3.9 18.2 - - - +
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Residues in contact with ILE 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 4.2 15.5 - - + -
24X GLY 3.5 11.4 - - - +
25X ILE* 4.5 7.2 - - + +
31X LYS* 1.3 76.1 - - - +
33X THR* 1.3 62.8 + - - +
34X ILE* 3.7 21.8 + - + -
49X MET 3.7 0.9 - - - +
50X ARG* 4.6 0.7 - - - -
51X PHE* 2.8 34.9 + - - +
53X ILE* 3.7 27.1 - - + -
59X MET* 4.0 12.3 - - + -
62X ILE* 3.8 26.7 - - + -
81X LEU* 3.7 26.7 - - + -
84X ILE* 4.3 5.4 - - + -
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Residues in contact with THR 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 3.7 1.0 - - - +
23X LYS* 2.8 39.2 + - + -
24X GLY* 2.8 25.3 + - - +
31X LYS* 5.2 2.8 - - - +
32X ILE* 1.3 72.4 + - - +
34X ILE* 1.3 55.1 + - - +
48X THR* 3.4 29.8 - - + -
49X MET 3.5 7.4 - - - +
50X ARG* 3.5 28.5 - - - +
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Residues in contact with ILE 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLY* 3.8 16.6 - - - -
21X VAL 3.5 11.9 - - - +
22X VAL* 4.6 6.7 - - + -
32X ILE* 3.8 17.7 - - + +
33X THR* 1.3 79.0 - - - +
35X HIS* 1.3 64.5 + - - +
36X HIS* 3.4 8.6 + - + +
47X MET 3.6 0.5 - - - +
48X THR* 3.3 3.0 - - - -
49X MET 2.9 30.6 + - - +
51X PHE* 3.8 28.0 - - + -
68X VAL* 4.4 2.5 - - + -
70X PHE* 3.8 36.3 - - + -
81X LEU* 4.9 0.9 - - + -
84X ILE* 3.9 27.6 - - + -
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Residues in contact with HIS 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20X GLY* 3.2 1.7 - - - -
21X VAL* 2.9 39.8 + - + +
23X LYS* 3.7 27.9 + - + +
34X ILE* 1.3 67.9 - - - +
36X HIS* 1.3 58.2 + - - +
46X GLU* 2.6 39.5 + - + +
47X MET* 3.4 16.7 - - - -
48X THR* 3.3 20.7 + - - +
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Residues in contact with HIS 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X THR 3.3 15.0 - - - +
20X GLY* 3.8 0.7 - - - -
34X ILE* 3.4 6.0 + - + -
35X HIS* 1.3 74.1 - - - +
37X ASP* 1.3 84.7 + - - +
39X ILE* 3.7 10.6 - - + +
44X TRP* 3.8 20.3 - + + -
45X PRO 3.2 23.1 + - - -
46X GLU* 3.2 29.1 - - - +
47X MET* 2.8 43.9 + - + +
49X MET* 3.7 28.7 - - + +
51X PHE* 4.0 11.2 - + - -
70X PHE* 4.2 15.3 - - + -
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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