Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 2RD0
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 ILE 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LYS* 5.2 1.3 - - - +
68A TYR* 1.3 80.2 - - - +
70A PHE* 1.3 77.9 + - - +
71A VAL* 4.3 3.4 - - + -
81A GLU* 3.9 26.9 - - + +
82A PHE 3.5 11.7 - - - +
83A PHE* 4.0 13.7 - - + +
85A GLU* 3.4 32.1 - - + +
100A LYS 3.6 0.2 - - - +
101A VAL* 3.6 2.7 - - - -
102A ILE* 2.7 40.3 + - + +
103A GLU 5.9 0.2 - - - -
104A PRO* 4.6 18.2 - - + -
109A GLU* 4.4 15.3 - - - +
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Residues in contact with PHE 70 (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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24A CYS* 4.7 2.2 - - - -
42A LEU* 3.6 29.2 - - + -
45A ILE* 4.4 4.7 - - + -
46A LYS* 3.5 50.0 - - + -
49A LEU* 3.9 25.4 - - + -
50A PHE* 5.8 0.2 - + - -
69A ILE* 1.3 73.9 - - - +
71A VAL* 1.3 58.8 + - - +
82A PHE* 2.6 49.9 + - + -
85A GLU* 3.4 23.1 + - - +
99A LEU* 3.6 36.3 - - + -
100A LYS 3.6 2.7 - - - -
101A VAL* 4.1 16.2 - - + -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.3 3.1 - - + -
70A PHE* 1.3 81.3 - - - +
72A SER* 1.3 68.2 + - - +
79A ARG* 4.5 12.8 - - + +
80A GLU 3.3 26.2 - - - +
81A GLU* 3.5 24.5 - - + +
82A PHE* 4.2 2.2 - - - -
99A LEU* 3.8 0.4 - - - -
100A LYS* 2.9 43.9 + - + +
102A ILE* 3.5 35.2 - - + -
493B ILE* 5.9 2.7 - - + -
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Residues in contact with SER 72 (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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71A VAL* 1.3 81.5 - - - +
73A VAL* 1.3 73.8 + - - +
74A THR* 3.7 1.6 + - - +
78A GLU 3.3 1.2 - - - +
79A ARG* 3.3 5.9 - - - -
80A GLU* 3.1 29.6 + - - +
82A PHE* 3.8 19.1 - - - -
94A LEU* 3.5 16.2 + - - +
98A PHE* 2.9 43.6 + - - -
99A LEU* 4.4 0.9 - - - -
493B ILE* 5.2 2.0 - - - -
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Residues in contact with VAL 73 (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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72A SER* 1.3 81.3 + - - +
74A THR* 1.3 70.5 + - - +
77A ALA 4.4 1.6 - - - -
78A GLU 3.1 13.2 - - - +
79A ARG* 4.4 3.4 - - + -
94A LEU* 2.7 29.7 - - - +
95A PHE* 3.8 4.9 - - + +
96A GLN 4.8 0.2 + - - -
98A PHE* 4.0 6.3 - - + -
486B ALA* 3.7 30.7 - - + +
489B GLU* 4.0 9.9 - - + -
490B THR* 3.5 30.1 - - - +
493B ILE* 3.8 25.6 - - + -
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Residues in contact with THR 74 (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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72A SER 4.5 0.4 - - - +
73A VAL* 1.3 80.3 - - - +
75A GLN* 1.3 54.4 + - - +
76A GLU* 3.0 9.2 + - - +
77A ALA* 2.7 30.1 + - - -
78A GLU* 2.8 37.9 + - - +
80A GLU* 3.3 35.9 - - + +
82A PHE* 4.4 9.0 - - + -
93A ARG* 3.2 37.0 - - - +
95A PHE* 4.2 1.8 - - - -
486B ALA* 4.5 0.2 - - - +
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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