Contacts of the strand formed by residues 34 - 40 (chain H) in PDB entry 2ZVW
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 GLY 34 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29H ASP 3.3 13.7 - - - +
31H SER* 3.1 19.8 + - - -
33H THR* 1.3 83.7 - - - +
35H PHE* 1.3 60.8 + - - -
36H SER* 3.6 2.3 + - - -
51H LEU* 4.6 7.2 - - - +
52H LEU 3.6 11.0 - - - -
53H ARG* 4.3 1.6 - - - -
54H SER 3.8 4.3 - - - -
60H TYR* 3.0 15.9 - - - -
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Residues in contact with PHE 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.5 26.7 - - + -
12H LEU* 4.5 13.7 - - + -
28H PHE* 3.3 52.9 - + + -
29H ASP 3.7 2.5 - - - -
30H CYS* 3.6 17.5 - - - +
34H GLY* 1.3 69.8 - - - -
36H SER* 1.3 59.3 + - - +
50H LEU* 4.8 3.3 - - + +
51H LEU* 3.7 0.7 + - - -
52H LEU* 2.8 60.0 + - + +
57H PHE* 4.0 16.2 - + + -
60H TYR* 3.3 6.9 + - - +
68H MET* 4.0 10.8 - - + -
75H MET* 4.8 5.2 - - + -
90H ILE* 3.8 20.2 - - + -
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Residues in contact with SER 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H PHE* 3.4 10.5 - - - -
29H ASP* 2.9 46.2 + - - +
34H GLY 3.6 2.1 + - - -
35H PHE* 1.3 75.2 - - - +
37H LEU* 1.3 68.4 + - - +
50H LEU* 3.2 17.7 - - - -
51H LEU* 3.9 15.7 - - - -
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Residues in contact with LEU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H VAL* 5.2 7.6 - - + -
26H ALA* 4.1 16.6 - - + -
27H ASN 3.3 20.0 - - - +
28H PHE* 3.4 37.9 - - + -
29H ASP* 4.5 4.5 - - - -
36H SER* 1.3 84.2 + - - +
38H GLN* 1.3 72.7 + - - +
39H ALA* 4.3 5.2 - - + +
48H VAL* 4.0 22.2 - - + -
49H SER* 3.6 2.8 + - - -
50H LEU* 2.9 46.8 + - + +
72H LEU* 4.6 8.5 - - + -
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Residues in contact with GLN 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H ALA* 5.1 0.9 - - - +
27H ASN 4.5 3.3 + - - +
37H LEU* 1.3 77.4 - - - +
39H ALA* 1.3 69.3 + - - +
47H LEU* 3.7 30.8 - - + +
48H VAL 3.3 4.5 - - - +
49H SER* 4.5 12.1 + - - +
123H SER* 4.8 4.2 - - - -
124H GLU 4.4 1.7 - - - +
125H HIS* 3.2 47.6 + - + +
126H LEU* 2.8 46.4 + - - +
128H ILE* 4.8 8.5 - - - +
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Residues in contact with ALA 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H VAL* 4.2 12.7 - - + +
25H ASP 5.1 1.3 - - - +
26H ALA* 3.9 26.2 - - + -
37H LEU* 4.3 5.2 - - + -
38H GLN* 1.3 81.0 - - - +
40H MET* 1.3 66.9 + - - +
47H LEU* 3.5 3.3 - - - -
48H VAL* 2.9 38.8 + - + +
123H SER* 5.7 5.4 - - - -
124H GLU 4.9 7.0 - - - -
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Residues in contact with MET 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E ASP* 4.9 9.0 + - - +
23H VAL* 4.0 15.7 - - - +
39H ALA* 1.3 79.5 - - - +
41H ASP* 1.3 71.6 + - - +
44H HIS* 3.6 37.2 - - + +
46H ALA 3.3 15.3 - - - +
47H LEU* 3.9 17.5 - - + -
124H GLU* 3.6 49.6 + - + +
126H LEU* 3.7 24.9 - - + -
147P MET* 3.9 13.7 - - - -
148P THR* 4.4 3.6 - - + -
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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