Contacts of the strand formed by residues 68 - 72 (chain G) in PDB entry 5EEZ
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63G ILE 3.9 0.2 - - - +
64G GLN* 3.6 2.3 - - - -
65G THR* 2.9 35.9 + - - +
66G ARG 3.3 2.2 + - - -
67G HIS* 1.3 83.2 - - - +
69G VAL* 1.4 66.7 + - - -
70G ILE* 3.9 0.9 + - - +
64H GLN* 4.6 3.5 - - - +
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Residues in contact with VAL 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G TYR* 3.5 44.9 - - + +
63G ILE 3.4 7.4 - - - +
64G GLN* 4.1 17.0 - - + +
68G GLY* 1.4 72.8 - - - -
70G ILE* 1.3 69.6 + - - +
71G GLU* 5.0 4.0 - - + +
62H TYR* 6.0 0.2 - - - -
64H GLN* 3.2 17.9 + - - -
50N GLU* 4.8 13.4 - - - +
50O GLU* 4.7 4.0 - - - +
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Residues in contact with ILE 70 (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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63G ILE* 2.8 60.7 + - + +
65G THR* 5.5 1.6 - - + -
68G GLY 5.3 1.3 - - - +
69G VAL* 1.3 76.6 - - - +
71G GLU* 1.3 65.9 + - - +
11H VAL* 4.0 24.5 - - + -
13H LYS* 3.9 31.9 - - + -
43H VAL* 4.4 6.3 - - + -
62H TYR* 3.8 31.6 - - + +
64H GLN* 4.0 19.1 - - - +
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Residues in contact with GLU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 4.0 9.4 - - - +
60G LYS* 5.3 2.6 - - - +
61G ALA 3.3 11.4 - - - +
62G TYR* 3.9 31.5 - - + -
69G VAL* 5.0 3.3 - - + +
70G ILE* 1.3 82.1 - - - +
72G SER* 1.3 63.2 + - - +
73G GLU* 5.0 6.6 - - + +
13H LYS* 3.0 39.0 + - - +
43H VAL* 4.1 3.9 - - - +
26O ARG 3.7 19.1 - - - +
27O GLY* 4.2 6.4 - - - -
28O ALA* 5.0 10.3 - - + +
29O ASP* 4.6 7.7 - - - +
31O ARG* 3.5 24.2 + - - -
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Residues in contact with SER 72 (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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57G VAL* 3.5 19.5 - - - +
59G GLY 2.7 22.1 + - - -
60G LYS* 3.4 6.6 - - - +
61G ALA* 3.0 38.0 + - - +
63G ILE* 3.9 8.8 - - - +
71G GLU* 1.3 76.9 - - - +
73G GLU* 1.3 66.1 + - - +
41H GLY 3.2 13.9 - - - -
43H VAL* 3.8 16.2 - - - -
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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