Contacts of the strand formed by residues 39 - 46 (chain H) in PDB entry 4UDW
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 GLU 39 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34H PHE* 3.4 11.2 - - - -
35H ARG* 2.9 67.2 + - + -
37H PRO* 3.2 25.1 + - + +
38H GLN* 1.3 74.7 - - - +
40H LEU* 1.3 69.8 + - - +
41H LEU* 4.0 5.8 - - + +
556I PHE* 3.9 11.7 - - + -
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Residues in contact with LEU 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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32H MET* 3.5 35.0 - - + -
33H LEU 4.0 2.2 - - - -
34H PHE* 4.4 3.6 - - - -
39H GLU* 1.3 82.8 - - - +
41H LEU* 1.3 60.8 + - - +
42H CYS 3.5 23.1 - - - +
73H ARG* 5.2 3.6 - - + +
141H TRP* 3.7 34.8 - - + +
142H GLY* 4.6 0.4 - - - -
193H GLY* 3.7 27.6 - - - +
556I PHE* 3.6 24.9 - - + -
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Residues in contact with LEU 41 (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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33H LEU* 2.8 21.9 + - + +
34H PHE 4.2 1.8 - - - +
35H ARG* 3.5 42.6 - - + +
39H GLU* 3.4 10.3 + - - +
40H LEU* 1.3 78.9 - - - +
42H CYS* 1.3 73.8 + - + +
58H CYS 5.2 4.5 - - - +
59H LEU* 6.2 0.2 - - + -
60H LYS* 3.7 44.8 + - + +
64H LEU* 3.2 34.8 - - + -
193H GLY* 5.0 6.5 - - - -
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Residues in contact with CYS 42 (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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32H MET* 3.8 0.9 - - - -
33H LEU* 2.8 33.7 + - + +
40H LEU* 3.5 11.7 - - - +
41H LEU* 1.3 87.7 - - + +
43H GLY* 1.3 64.5 + - - +
57H HIS* 5.0 0.7 - - - -
58H CYS* 2.1 59.0 - - + -
60H LYS* 5.7 2.0 - - - -
193H GLY* 3.8 13.7 - - - -
195H SER* 3.3 16.6 - - - +
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Residues in contact with GLY 43 (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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30H GLN* 5.2 4.3 - - - -
31H VAL 3.4 9.6 - - - -
32H MET* 4.8 0.7 - - - -
33H LEU* 3.9 0.7 - - - +
42H CYS* 1.3 77.9 - - - +
44H ALA* 1.3 62.9 + - - +
54H THR* 2.9 20.4 + - - -
141H TRP* 5.4 4.9 - - - -
193H GLY 3.7 6.8 + - - -
194H ASP* 4.6 2.0 - - - -
195H SER 2.8 12.5 + - - +
196H GLY 3.2 10.8 - - - -
197H GLY* 3.8 8.3 - - - -
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Residues in contact with ALA 44 (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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30H GLN* 3.9 2.1 + - - -
31H VAL* 2.9 31.2 + - + +
33H LEU* 3.8 13.2 - - + -
43H GLY* 1.3 76.0 - - - +
45H SER* 1.3 63.2 + - - +
52H VAL* 3.5 19.1 - - + -
53H LEU 3.2 15.5 - - - +
54H THR* 3.8 8.3 - - - -
196H GLY 3.3 10.3 + - - -
197H GLY* 3.8 2.1 - - - -
198H PRO* 3.9 10.4 - - - +
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Residues in contact with SER 45 (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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29H TRP* 3.2 10.8 - - - -
31H VAL* 3.8 5.2 - - - -
44H ALA* 1.3 78.2 - - - +
46H LEU* 1.3 61.5 + - - +
47H ILE* 3.7 2.1 + - - +
52H VAL* 3.2 6.4 - - - +
53H LEU* 2.8 45.3 + - - +
121H VAL* 4.6 7.2 - - - -
198H PRO* 4.2 13.2 - - - -
209H GLN* 2.6 34.5 + - - -
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Residues in contact with LEU 46 (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 PRO 4.8 0.2 - - - +
29H TRP* 2.8 21.6 + - - +
31H VAL* 3.7 7.1 - - + +
45H SER* 1.3 71.8 - - - +
47H ILE* 1.3 60.6 + - - +
48H SER 3.1 25.8 - - - +
51H TRP 3.8 8.1 - - - +
52H VAL* 4.0 13.9 - - + -
68H ILE* 4.3 12.6 - - + -
108H LEU* 4.8 2.9 - - + -
112H VAL* 4.1 15.0 - - + -
114H PHE* 4.1 11.9 - - + -
118H ILE* 3.8 28.9 - - + -
119H HIS 4.0 18.8 - - - +
120H PRO* 3.2 2.4 - - + +
121H VAL* 3.0 28.1 + - - +
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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