Contacts of the strand formed by residues 18 - 24 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71I PRO* 4.5 9.2 - - + +
72I THR* 3.5 19.8 - - - +
135I SER 6.0 1.3 - - - +
137I PRO* 5.7 0.9 - - + -
4J LEU* 3.6 28.7 - - + -
5J SER* 4.4 20.1 + - - +
8J ILE* 4.5 14.6 - - + -
16J LEU 4.1 2.4 + - - -
17J VAL* 1.3 77.8 - - - +
19J GLN* 1.3 63.0 + - - +
20J GLU 4.1 9.9 - - - +
21J SER* 3.8 20.9 - - - +
44J HIS* 3.5 30.3 - - + -
45J THR 3.9 5.4 - - - +
46J ALA* 4.1 4.9 - - + -
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Residues in contact with GLN 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I TYR* 3.2 22.6 - - - -
71I PRO* 3.3 13.5 - - - +
72I THR* 3.7 8.6 - - + +
75I HIS* 4.3 18.1 - - + +
89I PRO* 2.4 39.3 + - - +
90I TRP* 3.5 5.5 - - - +
91I PRO* 3.3 32.3 - - + +
92I ARG* 3.8 5.2 + - - +
17J VAL* 3.7 16.4 - - + +
18J ILE* 1.3 75.2 - - - +
20J GLU* 1.3 62.4 + - + +
45J THR 3.0 12.2 + - - +
47J TYR* 4.3 20.2 + - - +
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Residues in contact with GLU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I TYR* 4.0 17.9 - - + -
71I PRO* 4.4 2.9 - - - -
91I PRO* 3.8 3.5 - - + +
92I ARG* 3.3 8.8 + - - +
93I SER* 2.3 55.5 + - - -
193I SER* 3.5 10.4 + - - -
18J ILE* 3.8 1.8 - - - +
19J GLN* 1.3 86.0 - - + +
21J SER* 1.3 65.7 + - - +
22J ILE* 3.3 24.6 - - + +
43J VAL 3.4 1.1 - - - +
44J HIS* 3.2 3.3 - - - -
45J THR* 2.9 50.9 + - - +
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Residues in contact with SER 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I GLN* 3.9 6.4 - - - +
68I ASP* 4.4 11.3 - - - +
71I PRO* 4.2 5.8 - - - +
137I PRO* 3.3 32.3 - - - +
138I ALA* 6.1 0.3 - - - +
18J ILE* 3.8 6.9 - - - +
20J GLU* 1.3 76.6 + - - +
22J ILE* 1.3 66.4 + - - +
23J LEU 3.8 2.1 + - - -
42J LEU* 4.1 10.3 - - - +
43J VAL 3.6 5.6 - - - -
44J HIS* 3.0 33.5 - - - -
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Residues in contact with ILE 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I GLN* 3.5 15.7 - - + +
70I TYR* 6.2 0.7 - - + -
81I PHE* 5.8 1.8 - - + -
93I SER* 4.2 1.6 - - - +
191I HIS* 3.4 54.3 - - + +
193I SER* 4.0 10.5 - - - +
20J GLU* 3.3 32.5 - - + +
21J SER* 1.3 82.1 - - - +
23J LEU* 1.3 68.3 + - - +
24J MET* 4.4 7.0 - - + -
41J ILE 3.3 2.4 - - - +
42J LEU* 3.2 2.4 - - - -
43J VAL* 2.5 45.3 + - + +
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Residues in contact with LEU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I GLN* 2.7 36.4 + - - +
141I ARG* 3.4 33.7 - - - +
169I GLY* 6.0 1.0 - - - -
170I ARG 5.6 0.3 + - - -
171I ASP* 3.8 27.9 + - + +
21J SER 3.8 1.0 + - - -
22J ILE* 1.3 72.9 - - - +
24J MET* 1.3 65.3 + - - +
25J LEU* 5.8 2.2 - - + -
28J GLU* 4.5 2.1 - - - +
40J ASP* 3.6 36.8 - - + +
41J ILE 3.4 15.9 - - - +
42J LEU* 3.8 21.7 - - + +
61J ASP* 5.1 6.5 - - + -
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Residues in contact with MET 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I GLY* 5.1 0.9 - - - -
171I ASP 5.9 0.7 - - - +
191I HIS* 3.7 20.4 - - + -
193I SER* 5.2 2.9 - - - -
195I LEU* 3.9 17.3 - - - -
196I SER* 3.2 29.8 - - - +
22J ILE* 4.0 6.3 - - + +
23J LEU* 1.3 79.6 - - - +
25J LEU* 1.3 69.4 + - - +
28J GLU* 3.3 44.9 - - + +
29J VAL* 4.1 9.2 - - + -
40J ASP* 3.5 4.2 - - - +
41J ILE* 2.8 35.0 + - - +
43J VAL* 3.6 29.6 - - + -
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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