Contacts of the strand formed by residues 51 - 55 (chain A) in PDB entry 5XFR
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 ASP 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLY 3.6 4.4 + - - +
50A GLN* 1.3 78.8 + - - +
52A VAL* 1.3 64.1 + - - +
63A LEU* 4.8 14.1 - - + -
64A GLY 3.4 4.3 - - - +
65A THR* 2.5 35.1 + - - +
96A GLY* 4.8 5.0 + - - -
97A ALA 3.8 12.7 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 5.0 1.1 - - + -
50A GLN* 4.0 25.4 - - + +
51A ASP* 1.3 79.5 - - - +
53A LEU* 1.3 65.1 + - - +
54A ALA* 4.8 0.7 - - + +
63A LEU* 3.6 6.4 - - - +
64A GLY 2.8 40.7 + - - +
66A ILE* 4.0 22.9 - - + -
78A ILE* 4.0 27.6 - - + -
93A ILE* 3.9 20.2 - - + -
94A GLN 3.8 11.4 - - - +
95A THR* 4.8 3.6 - - - -
97A ALA 4.2 5.8 - - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 1.3 74.8 - - - +
54A ALA* 1.3 59.5 + - - +
61A PHE* 3.6 20.1 - - + -
62A TYR* 3.5 5.2 - - - +
63A LEU* 4.1 25.4 - - + +
93A ILE* 3.6 2.4 - - - +
94A GLN* 2.7 74.0 + - + +
96A GLY 4.0 8.0 + - - +
97A ALA* 3.8 26.9 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.9 2.4 + - + -
53A LEU* 1.3 72.8 - - - +
55A ARG* 1.3 60.9 + - - +
56A TRP 3.5 2.1 + - - -
61A PHE* 3.3 1.7 - - - -
62A TYR* 2.7 41.8 + - - +
64A GLY 5.6 0.2 - - - +
78A ILE* 3.7 31.2 - - + -
80A PHE* 3.8 25.3 - - + -
88A VAL* 4.2 9.4 - - + -
92A ASP 3.5 3.6 - - - -
93A ILE* 4.7 1.6 - - + +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 1.3 70.2 - - - +
56A TRP* 1.3 73.2 + - - +
59A GLY* 3.9 22.1 + - - +
60A LEU 3.4 6.1 - - - +
61A PHE* 3.5 42.3 - - + -
80A PHE* 6.4 0.2 - - - -
88A VAL* 4.2 8.9 - - - +
91A LYS 3.8 12.1 + - - -
92A ASP* 2.8 53.0 + - + +
206A CYS* 3.4 37.2 + - - +
207A GLY 3.9 3.0 + - - -
208A GLY* 3.5 25.5 - - - +
209A PRO* 3.8 7.6 - - - +
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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