Contacts of the strand formed by residues 55 - 60 (chain f) in PDB entry 5M32
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 GLN 55 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53f VAL* 5.3 4.6 - - + +
54f GLY* 1.3 81.2 - - - +
56f ILE* 1.3 59.1 + - - +
99f ALA* 3.3 26.8 - - + +
100f LEU 3.3 15.3 - - - +
101f ASP* 4.9 4.0 - - - +
102f MET* 4.0 1.5 - - - +
108f MET* 3.4 37.2 - - + +
109f ARG* 4.9 3.0 - - - +
132g TYR* 3.4 3.6 - - - -
133g PHE* 2.5 63.5 + - + +
135g PRO* 5.6 7.4 - - + +
80q THR* 5.7 6.7 - - - -
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Residues in contact with ILE 56 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55f GLN* 1.3 74.5 - - - +
57f VAL* 1.3 61.1 + - - +
73f ALA* 5.4 4.3 - - + -
79f TYR* 3.7 23.1 - - - +
99f ALA* 3.3 2.3 - - - -
100f LEU* 2.5 59.7 + - + +
101f ASP 4.0 10.1 - - - +
102f MET* 3.8 22.6 - - + +
105f LEU* 4.4 8.3 - - + -
131g THR 4.9 0.4 - - - +
132g TYR* 3.5 36.6 - - + +
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Residues in contact with VAL 57 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56f ILE* 1.3 81.0 - - - +
58f GLY* 1.3 59.2 + - - +
73f ALA* 4.0 14.9 - - - +
74f THR* 3.7 13.9 + - + +
97f ARG* 4.1 18.6 - - + +
98f VAL 3.4 7.4 - - - +
99f ALA* 4.8 0.7 - - - -
100f LEU* 4.6 3.7 - - - +
111f LEU* 3.9 16.6 - - + -
123g VAL* 4.5 1.3 - - + -
131g THR* 3.3 37.9 + - + +
132g TYR 4.2 1.6 - - - -
133g PHE* 3.6 37.2 - - + +
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Residues in contact with GLY 58 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57f VAL* 1.3 80.0 - - - +
59f GLU* 1.3 59.2 + - - -
71f VAL* 5.2 1.1 - - - -
72f LYS 3.3 11.2 - - - -
73f ALA* 4.0 6.3 - - - -
74f THR* 4.8 4.0 - - - -
97f ARG* 3.3 6.3 - - - +
98f VAL* 2.7 39.6 + - - +
100f LEU* 4.5 7.4 - - - -
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Residues in contact with GLU 59 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58f GLY* 1.3 74.2 - - - -
60f VAL* 1.3 61.6 + - - +
61f LEU* 2.9 11.8 - - + +
71f VAL* 4.1 1.8 - - - -
72f LYS* 2.5 51.6 + - + +
95f GLY* 3.3 32.5 - - - +
96f THR 3.4 8.5 - - - +
97f ARG* 5.1 4.3 - - + +
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Residues in contact with VAL 60 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58f GLY 4.2 0.6 - - - -
59f GLU* 1.3 69.3 - - - +
61f LEU* 1.3 55.2 + - - +
62f LYS* 2.4 43.4 + - + +
64f LEU* 5.6 0.2 - - + -
69f PHE* 4.4 18.4 - - + -
70f ILE 4.0 4.0 - - - +
71f VAL* 3.8 20.8 - - + +
92f LEU* 5.1 9.9 - - + +
93f LYS 3.4 20.2 - - - +
95f GLY 3.1 16.0 + - - -
96f THR* 3.2 24.3 + - - +
98f VAL* 4.2 11.3 - - + +
107f ILE* 5.7 1.8 - - + -
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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