Contacts of the strand formed by residues 34 - 39 (chain I) in PDB entry 2ZPK
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 MET 34 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4I LEU* 3.7 31.6 - - + -
22I CYS* 4.2 8.3 - - - -
24I ALA* 4.5 2.9 - - + -
27I TYR* 3.6 24.0 - - - +
29I PHE* 4.1 18.8 - - + -
32I ALA 5.7 0.2 - - - +
33I GLY* 1.3 72.6 - - - -
35I GLN* 1.3 67.2 + - - +
36I TRP* 4.3 6.2 - - - +
50I TRP* 3.2 2.3 - - - +
51I ILE* 2.9 51.0 + - + +
52I THR* 4.2 9.8 + - - +
78I ALA* 4.0 17.5 - - + -
92I CYS* 4.2 9.4 - - + -
93I ALA 3.9 17.0 - - - -
94I ARG* 3.9 6.3 - - + -
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Residues in contact with GLN 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I MET* 1.3 78.4 - - - +
36I TRP* 1.3 66.5 + - - +
47I TRP* 2.7 28.8 + - - -
49I GLY 3.4 6.1 - - - +
50I TRP* 3.6 15.9 - - + +
92I CYS* 3.4 5.7 - - - -
93I ALA* 2.8 42.1 + - - +
95I GLU* 3.4 30.4 + - + -
98I GLY* 2.9 32.2 + - - +
99I PHE* 3.7 21.7 - - + -
96M TRP* 3.5 8.1 - - - +
4Q TYR* 3.5 7.9 + - - -
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Residues in contact with TRP 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 4.3 3.4 - - - -
20I ILE* 3.9 24.0 - - + -
21I SER 4.5 0.2 - - - -
22I CYS* 3.7 24.0 - - + -
34I MET* 4.3 15.7 + - + +
35I GLN* 1.3 78.1 + - - +
37I VAL* 1.3 60.6 + - - +
47I TRP* 3.8 2.3 - - - -
48I ILE* 2.8 42.1 + - + +
49I GLY 3.0 8.6 + - - +
51I ILE* 4.7 3.0 - - + +
69I PHE* 3.5 44.8 - + + +
78I ALA* 3.8 16.9 - - + +
79I TYR 3.7 9.1 + - - -
80I LEU* 3.6 47.8 - - + -
90I TYR* 5.1 0.7 - - + -
91I PHE* 3.3 24.0 - - - -
92I CYS* 3.7 17.0 - - + -
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Residues in contact with VAL 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I TRP* 1.3 80.1 - - - +
38I GLN* 1.3 63.3 + - - +
45I LEU* 3.7 38.1 - - + -
46I LYS 3.4 13.2 - - - +
47I TRP* 4.9 0.2 - - - -
48I ILE* 3.9 5.3 - - - +
89I THR 4.0 0.2 - - - +
90I TYR* 3.3 7.3 - - - +
91I PHE* 2.8 44.1 + - + +
93I ALA* 5.0 3.1 - - + -
99I PHE* 3.6 36.1 - - + -
103I TRP* 4.2 11.7 - - + -
98M PHE* 4.0 10.3 - - + -
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Residues in contact with GLN 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I VAL* 1.3 75.0 - - - +
39I LYS* 1.3 63.7 + - - +
40I MET* 3.2 40.2 + - + +
44I SER 4.2 0.9 - - - +
45I LEU* 3.5 4.5 - - - -
46I LYS* 2.8 52.8 + - + +
48I ILE* 3.9 8.9 - - + +
63I PHE* 3.5 27.4 - - + -
67I PHE* 4.5 4.6 - - - -
85I GLU 4.5 2.4 + - - -
86I ASP* 4.6 1.6 + - - +
88I ALA* 3.7 11.5 - - + +
89I THR 3.7 2.2 - - - -
90I TYR* 3.0 40.6 + - + -
91I PHE* 5.4 0.2 - - - -
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Residues in contact with LYS 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I GLN* 1.3 75.0 - - - +
40I MET* 1.3 64.7 + - - +
41I PRO 4.0 0.3 - - - -
42I GLY 4.3 9.9 + - - +
43I LYS 2.5 35.1 + - - +
44I SER* 4.4 4.0 - - - +
45I LEU* 3.9 29.6 - - + +
88I ALA* 3.5 3.2 - - - -
89I THR* 2.7 41.2 + - - +
91I PHE* 4.1 8.1 - - + -
38M GLU* 4.7 12.1 - - - -
42M HIS* 4.1 27.4 - - + +
44M PHE* 4.7 6.7 - - + -
87M PHE* 5.1 9.3 - - - -
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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