Contacts of the strand formed by residues 59 - 62 (chain G) in PDB entry 5U07
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 ALA 59 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ARG* 3.5 29.7 + - - +
52G GLU* 4.2 8.0 + - - +
57G ASP 4.1 0.4 + - - -
58G LYS* 1.3 74.6 - - - +
60G VAL* 1.3 68.2 + - - +
118G TYR* 3.7 19.5 - - + +
119G LEU 3.9 5.6 - - - +
120G PRO* 4.1 1.1 - - - -
164G ASN* 3.0 22.6 - - + +
166G SER* 4.2 6.5 - - - -
167G VAL* 4.8 2.9 - - + -
209H ASP* 3.8 4.2 - - - +
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Residues in contact with VAL 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ALA* 1.3 79.8 - - - +
61G ARG* 1.3 59.8 + - - +
62G THR* 3.4 34.0 + - + +
65G ILE* 5.6 0.4 - - + -
117G PHE 3.0 5.9 - - - +
118G TYR* 4.1 2.5 - - - -
119G LEU* 2.9 37.2 + - + +
121G VAL* 3.5 26.0 - - + -
124G ILE* 4.5 19.3 - - + -
209H ASP* 3.5 9.9 - - + +
210H ILE* 4.4 11.4 - - + -
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Residues in contact with ARG 61 (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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48G ARG* 5.3 9.7 - - - +
60G VAL* 1.3 69.8 - - - +
62G THR* 1.3 58.8 + - - +
116G LEU* 3.6 29.3 + - + +
117G PHE 2.9 9.0 - - - +
118G TYR* 3.4 56.5 - - + +
171G GLY 4.9 4.0 + - - -
172G ARG* 5.8 1.0 - - - +
173G MET 5.9 2.6 + - - +
206H ALA* 5.1 1.6 - - - -
207H VAL* 3.5 18.9 - - + +
208H ASP* 3.6 0.9 - - - -
209H ASP* 2.6 40.5 + - - +
18K A 3.5 22.0 + - - -
19K G 4.1 24.5 + - - -
20K U 4.4 15.9 + - - -
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Residues in contact with THR 62 (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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60G VAL* 3.4 24.6 - - + +
61G ARG* 1.3 80.4 - - - +
63G ARG* 1.3 63.2 + - - +
64G ARG 4.0 7.6 - - - -
65G ILE* 4.3 19.2 + - - +
116G LEU* 4.2 2.2 - - - -
117G PHE* 2.9 37.0 + - - +
124G ILE* 5.6 0.2 - - - +
208H ASP* 3.1 6.3 - - - +
209H ASP 3.6 2.2 - - - +
210H ILE* 3.3 46.8 - - + +
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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