Contacts of the strand formed by residues 31 - 38 (chain B) in PDB entry 4ZDH
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 ASN 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A TRP* 3.0 27.6 + - - +
98A GLY* 4.4 4.6 - - - -
29B HIS* 4.2 1.0 - - - +
30B GLU* 1.3 78.0 - - - +
32B MET* 1.3 67.4 + - - +
33B PHE* 3.5 13.8 - - + -
49B SER 3.3 5.8 - - - +
50B TYR* 3.6 31.4 - - - +
93B SER* 3.1 6.4 - - - -
94B SER* 2.9 59.0 + - - +
95B PHE* 4.0 9.4 - - - +
96B LEU* 4.6 1.0 - - - +
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Residues in contact with MET 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B CYS* 3.5 42.4 - - - +
25B GLN* 3.7 23.8 - - + +
30B GLU 3.9 0.8 + - - -
31B ASN* 1.3 80.0 - - - +
33B PHE* 1.3 65.7 + - - +
48B PHE* 3.3 2.4 - - - +
49B SER 2.9 33.5 + - - +
68B ARG* 3.6 20.8 - - - +
71B LYS 3.6 23.8 - - - +
72B GLU 4.0 3.8 - - - +
74B PHE* 3.5 33.3 - - + -
92B ALA 3.3 6.5 - - - +
93B SER* 3.9 9.6 - - - -
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLY 4.2 7.6 - - - -
99A LYS* 4.3 18.2 - - + -
100A LEU 5.5 0.4 - - - -
31B ASN* 3.5 29.4 - - + -
32B MET* 1.3 75.7 - - - +
34B TRP* 1.3 61.0 + - - +
35B TYR* 3.7 24.5 - - + -
45B LEU* 4.0 9.6 - - + -
47B TYR 3.6 5.4 - - - -
48B PHE* 3.5 32.5 - + + -
49B SER 5.4 0.4 - - - -
50B TYR* 4.9 2.9 - + - -
74B PHE* 4.0 3.8 - - - -
91B CYS* 3.2 8.7 - - - +
92B ALA* 2.9 39.9 + - + +
94B SER* 3.5 20.6 - - - -
102B GLN* 3.4 37.9 - - + -
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Residues in contact with TRP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLN* 3.7 25.1 - - + -
21B LEU* 3.7 31.9 - - + -
22B GLU 4.5 1.3 - - - -
23B CYS* 3.6 19.7 - - + +
33B PHE* 1.3 72.5 - - - +
35B TYR* 1.3 65.8 + - - +
45B LEU* 3.4 6.8 - - - +
46B ILE* 2.8 35.6 + - + -
47B TYR* 2.9 16.6 + - + +
66B VAL* 4.5 3.6 - - + -
74B PHE* 2.9 49.1 + + + -
76B LEU* 3.4 41.0 - - + +
89B TYR* 3.8 15.9 - - + -
90B LEU 3.5 20.6 - - - -
91B CYS* 3.7 22.2 - - + -
108B THR* 5.1 0.4 - - - -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU 4.5 6.5 + - - -
102A PHE* 3.5 25.8 - + + -
33B PHE* 3.7 19.3 - - + +
34B TRP* 1.3 75.6 - - - +
36B ARG* 1.3 60.7 + - - +
43B LEU* 3.6 27.6 - - + -
44B ARG 3.2 11.4 - - - +
45B LEU* 3.6 39.4 - - + +
46B ILE* 4.0 4.7 - - - +
89B TYR* 3.4 9.0 - - - +
90B LEU* 2.8 39.4 + - + +
92B ALA* 4.2 2.7 - - + -
102B GLN* 2.6 37.9 + - - -
104B PHE* 3.8 23.3 - + - -
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 1.3 75.3 - - - +
37B GLN* 1.3 60.3 + - - +
38B ASP* 2.9 36.6 + - - +
42B GLY 3.6 1.0 - - - +
43B LEU* 3.4 3.8 - - - -
44B ARG* 3.0 42.8 + - - +
46B ILE* 4.0 2.8 - - + +
60B ILE* 3.6 29.8 - - + -
64B TYR* 3.0 30.4 + - - -
84B ASP* 2.9 29.7 + - - -
85B GLN* 3.7 6.0 - - - +
86B THR 3.3 11.9 + - - -
87B SER* 3.2 14.3 + - - +
88B MET 3.2 6.7 - - - +
89B TYR* 3.9 14.4 - - + -
90B LEU 5.5 0.2 - - - -
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Residues in contact with GLN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLN* 2.7 45.0 + - - -
87A THR* 5.1 4.6 - - - +
89A LEU* 4.2 17.8 - - - +
36B ARG* 1.3 76.8 - - - +
38B ASP* 1.3 66.1 + - - +
39B PRO* 4.8 0.3 - - - +
42B GLY* 3.4 18.7 - - - +
43B LEU* 3.9 18.9 - - + +
87B SER* 3.1 11.3 + - - -
88B MET* 2.7 38.8 + - + +
90B LEU* 3.9 5.5 - - + +
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG* 2.9 40.3 + - - +
37B GLN* 1.3 76.1 - - - +
39B PRO* 1.3 77.3 - - + +
40B GLY 3.2 0.2 + - - -
41B LEU* 3.2 16.5 + - + -
42B GLY* 3.1 26.9 + - - -
44B ARG* 3.1 14.6 + - - -
86B THR 3.6 4.5 - - - +
87B SER* 2.6 24.9 + - - -
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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