Contacts of the strand formed by residues 68 - 72 (chain J) in PDB entry 5EEY
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 GLY 68 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63J ILE 3.8 0.2 - - - +
64J GLN* 3.5 2.4 - - - -
65J THR* 2.9 36.1 + - - +
66J ARG 3.4 1.4 - - - -
67J HIS* 1.3 77.9 - - - +
69J VAL* 1.3 66.7 + - - -
70J ILE* 4.0 0.9 + - - +
64K GLN* 4.5 3.9 - - - +
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Residues in contact with VAL 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J TYR* 3.6 47.1 - - + +
63J ILE 3.2 10.3 - - - +
64J GLN* 4.4 10.1 - - + +
68J GLY* 1.3 77.9 - - - -
70J ILE* 1.3 71.5 + - - +
71J GLU* 4.8 3.1 - - + -
64K GLN* 3.1 18.4 + - - +
50L GLU* 4.7 4.0 - - - +
50V GLU* 4.8 11.0 - - - +
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Residues in contact with ILE 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J ILE* 2.8 55.0 + - + +
65J THR* 5.7 1.3 - - + -
68J GLY 5.4 1.3 - - - +
69J VAL* 1.3 76.5 - - - +
71J GLU* 1.3 69.5 + - - +
11K VAL* 4.0 24.0 - - + -
13K LYS* 3.8 34.3 - - + +
43K VAL* 4.3 10.3 - - + -
62K TYR* 3.7 32.3 - - + +
64K GLN* 3.8 19.5 - - + +
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Residues in contact with GLU 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 3.8 22.2 - - - +
60J LYS* 5.4 1.6 + - - +
61J ALA 3.4 7.2 - - - +
62J TYR* 3.9 28.8 - - + -
69J VAL* 4.8 2.9 - - + +
70J ILE* 1.3 84.0 - - - +
72J SER* 1.3 64.3 + - - +
73J GLU* 5.5 1.8 - - + -
13K LYS* 2.9 40.4 + - - +
43K VAL* 4.4 3.6 - - - -
26L ARG 3.9 17.0 - - - +
27L GLY* 3.9 12.1 - - - -
28L ALA* 4.0 10.0 + - + -
29L ASP* 4.7 5.4 + - - +
31L ARG* 3.9 15.4 + - - -
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Residues in contact with SER 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J VAL* 3.5 23.1 - - - +
59J GLY 2.6 23.6 + - - -
60J LYS* 3.4 5.5 - - - +
61J ALA* 3.1 30.3 + - - +
63J ILE* 4.0 8.8 - - - +
71J GLU* 1.3 77.8 - - - +
73J GLU* 1.4 63.6 + - - +
41K GLY 3.2 14.8 - - - -
43K VAL* 3.7 16.9 - - - +
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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