Contacts of the strand formed by residues 48 - 52 (chain C) in PDB entry 3UGV
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 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ILE 3.6 0.7 - - - +
39C ASP* 3.5 5.2 - - - +
40C ILE* 2.8 40.4 + - - +
47C PRO* 1.3 75.9 - - - +
49C ARG* 1.3 63.4 + - - +
50C ALA 4.4 0.2 - - - -
111C ALA* 3.6 18.6 - - - -
114C ASP* 3.2 8.3 - - - -
115C ALA* 3.8 7.0 - - - -
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE 3.5 3.1 - - - -
39C ASP* 3.2 24.4 + - - +
47C PRO* 3.6 29.0 - - + +
48C GLY* 1.3 74.3 - - - +
50C ALA* 1.3 62.4 + - - +
111C ALA* 4.5 0.9 - - - -
114C ASP* 2.7 27.4 + - - +
118C ARG* 3.7 22.1 - - - +
352C LEU* 3.6 7.8 - - - +
354C LEU* 3.0 36.1 + - + +
355C ASP* 3.5 22.8 + - - +
356C TRP* 3.3 41.3 - - + +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 2.9 35.5 + - + +
49C ARG* 1.3 76.0 - - - +
51C TYR* 1.3 63.9 + - - +
107C GLY 4.6 2.9 - - - +
110C MET* 3.7 20.4 - - + +
111C ALA* 3.5 29.6 - - + +
309C VAL* 5.7 0.9 - - + -
352C LEU* 4.2 8.1 - - + -
354C LEU* 4.2 9.2 - - - -
356C TRP* 3.7 5.3 - - - -
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Residues in contact with TYR 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 4.2 8.1 - - + -
36C ILE 3.4 13.7 - - - +
37C LEU* 4.5 5.4 - - + -
38C ILE* 5.0 1.3 - - - -
50C ALA* 1.3 78.2 - - - +
52C LEU* 1.3 64.4 + - - +
53C GLU* 3.3 38.9 + - + -
107C GLY* 5.8 0.4 - - - -
110C MET* 3.8 9.0 - - - +
306C TYR* 3.1 32.0 - + + -
307C PRO* 3.8 15.6 - - - +
308C GLU* 2.7 31.4 + - - -
309C VAL* 6.1 3.7 - - + +
329C ALA* 3.6 24.6 - - + +
332C ILE* 4.6 4.7 - - + -
333C LEU* 4.8 7.4 - - + -
354C LEU* 3.8 23.6 - - + -
356C TRP* 4.1 16.8 - + + -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.4 8.8 - - - +
36C ILE* 3.0 46.9 + - + -
38C ILE* 4.1 12.3 - - + -
51C TYR* 1.3 73.8 - - - +
53C GLU* 1.3 64.6 + - - +
54C PRO* 3.5 8.5 - - + +
63C LEU* 4.8 2.7 - - + -
67C LEU* 4.5 15.3 - - + -
103C ILE* 3.7 26.7 - - + +
104C ALA* 4.9 1.8 - - - -
107C GLY* 3.7 31.6 - - - +
110C MET* 3.8 10.8 - - + -
279C MET* 3.7 31.4 - - + -
306C TYR* 3.9 1.1 - - - +
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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