Contacts of the strand formed by residues 32 - 37 (chain G) in PDB entry 5U2V
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 LEU 32 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G CYS* 4.3 1.6 - - - -
24G TYR* 3.9 18.8 - - + -
29G PHE* 4.0 9.2 - - + -
31G GLY* 1.3 74.4 - - - +
33G PHE* 1.3 69.0 + - - +
34G TRP* 3.5 34.8 - - + +
47G SER* 3.9 0.5 + - - +
48G TYR* 3.3 4.8 - - - -
49G ASN* 2.7 42.2 + - + +
64G LEU* 4.6 5.4 - - + -
71G SER* 3.5 27.4 - - - +
88G CYS* 4.0 15.5 - - - -
89G ALA 3.5 5.2 - - - +
90G VAL* 3.7 23.1 - - + -
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Residues in contact with PHE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G GLY 4.5 2.9 - - - -
32G LEU* 1.3 83.4 - - - +
34G TRP* 1.3 60.8 + - - +
35G TYR* 3.6 27.4 - + + -
45G PHE* 3.7 24.5 - + - -
47G SER 3.2 4.3 - - - -
48G TYR* 3.3 31.4 - + - -
87G LEU 3.7 0.2 - - - +
88G CYS* 3.6 4.0 - - - -
89G ALA* 2.7 44.2 + - + +
91G LYS* 4.1 17.9 - - + -
97G LEU* 4.3 12.1 - - + -
100H GLY 3.5 17.5 - - - -
101H SER 3.6 13.7 - - - -
102H GLY 3.7 13.5 - - - -
103H GLU* 3.8 16.6 - - + -
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Residues in contact with TRP 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G GLN* 3.7 25.6 - - - -
20G ILE* 3.4 41.7 - - + -
21G ASN 4.2 0.9 - - - -
22G CYS* 3.6 25.1 - - + -
32G LEU* 3.5 18.8 - - + +
33G PHE* 1.3 74.3 - - - +
35G TYR* 1.3 59.4 + - - +
45G PHE* 3.8 1.7 - - - -
46G LEU* 2.7 38.2 + - + -
47G SER* 2.9 33.2 + - - +
49G ASN* 5.3 0.7 - - - -
62G SER* 4.4 6.7 - - - -
71G SER* 3.2 20.4 + - - -
72G TYR* 4.0 5.5 - - - -
73G LEU* 3.6 28.5 - - + -
86G TYR* 3.8 24.2 - - + -
87G LEU 3.4 18.2 - - - -
88G CYS* 4.0 5.4 - - + -
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Residues in contact with TYR 35 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33G PHE* 3.6 29.6 - + + -
34G TRP* 1.3 77.8 - - - +
36G GLN* 1.3 60.0 + - - +
43G PRO* 4.1 22.9 - - + -
44G THR* 3.3 12.1 - - - +
45G PHE* 3.5 27.4 - - + -
46G LEU* 4.2 4.0 - - - -
86G TYR* 3.3 6.8 - - - +
87G LEU* 2.8 43.5 + - + +
89G ALA* 4.9 1.6 - - + -
97G LEU* 5.2 2.9 - - + +
99G TRP* 3.5 32.5 - + - -
103H GLU* 3.6 7.4 - - - +
104H LEU* 2.8 47.3 + - + +
106H PHE* 4.0 10.5 - + - -
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Residues in contact with GLN 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G TYR* 1.3 73.5 - - - +
37G GLN* 1.3 62.5 + - - +
38G HIS* 3.3 33.6 + - + +
42G ALA 3.9 1.2 - - - +
43G PRO* 3.2 1.3 - - - +
44G THR* 2.8 46.1 + - - +
46G LEU* 3.7 25.0 - - + +
60G PHE* 4.1 14.6 - - - -
81G LYS 4.7 4.0 + - - -
82G ASP* 4.8 2.2 + - - +
84G ALA* 3.9 11.2 - - + +
85G SER 3.6 2.9 - - - -
86G TYR* 3.2 32.5 + - + -
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Residues in contact with GLN 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G GLN* 1.3 75.1 - - - +
38G HIS* 1.3 64.9 + - - +
39G ALA* 3.8 0.9 + - - -
40G GLY 6.0 0.4 - - - +
41G GLU 2.9 29.0 + - - +
42G ALA 4.0 1.6 - - - -
43G PRO* 3.9 23.9 - - + +
84G ALA* 4.0 1.6 - - - -
85G SER* 2.6 47.7 + - - +
87G LEU* 3.7 15.9 - - + +
37H GLN* 2.9 42.6 + - - -
90H PHE* 3.7 11.1 - - - -
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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