Contacts of the strand formed by residues 61 - 65 (chain H) 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 ALA 61 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 3.8 23.8 - - + -
13H LYS 3.2 15.7 - - - +
15H LEU* 3.8 8.3 - - - -
19H VAL* 4.3 6.5 - - + -
57H VAL* 4.0 7.9 - - + -
59H GLY 3.3 1.2 + - - +
60H LYS* 1.3 76.5 - - - +
62H TYR* 1.3 60.7 + - - +
63H ILE* 3.9 1.9 + - + +
71H GLU* 3.4 6.6 - - - +
72H SER* 3.1 42.9 + - - +
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Residues in contact with TYR 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G VAL 6.0 0.2 - - - -
70G ILE* 3.8 21.4 - - + +
11H VAL 3.8 0.9 - - - +
12H ILE* 3.6 1.2 - - - -
13H LYS* 2.8 45.4 + - + +
15H LEU* 3.8 16.0 - - + +
61H ALA* 1.3 72.5 - - - +
63H ILE* 1.3 61.8 + - - +
64H GLN* 4.3 13.6 + - + -
69H VAL* 3.7 38.1 - - + +
70H ILE 4.2 1.6 - - - -
71H GLU* 4.1 22.9 - - + -
26N ARG 6.0 1.8 - - - -
31N ARG* 6.3 0.4 - - - -
50N GLU* 2.7 38.6 + - - +
51N HIS* 4.8 19.0 + + - -
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H VAL* 4.8 2.2 - - + -
11H VAL 3.2 8.7 - - - +
12H ILE* 4.1 22.9 - - + -
57H VAL* 4.0 21.1 - - + -
61H ALA 4.3 1.3 - - - +
62H TYR* 1.3 80.6 - - - +
64H GLN* 1.3 66.0 + - - +
65H THR* 4.1 22.0 - - + -
68H GLY 3.8 0.2 - - - +
69H VAL* 3.5 6.9 - - - +
70H ILE* 3.1 45.2 + - + +
72H SER* 3.7 34.3 - - - +
43I VAL* 4.2 14.4 - - + -
45I ILE* 4.8 10.3 - - + -
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Residues in contact with GLN 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G THR* 4.6 2.4 + - - -
67G HIS* 3.8 36.2 + - + +
68G GLY* 4.6 2.4 - - - +
69G VAL 3.2 24.1 + - - +
70G ILE* 4.0 20.0 - - + +
10H VAL* 3.5 4.9 - - - +
11H VAL* 2.8 62.2 + - + +
62H TYR* 4.3 14.8 + - + -
63H ILE* 1.3 77.5 - - - +
65H THR* 1.3 64.5 + - - +
68H GLY 3.7 5.4 - - - +
69H VAL* 4.3 15.1 - - + +
50N GLU* 4.5 5.7 + - - -
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Residues in contact with THR 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G HIS* 3.8 17.9 + - - +
9H PHE 4.6 2.9 - - - -
10H VAL* 4.2 18.2 - - + -
63H ILE* 4.1 16.8 - - + -
64H GLN* 1.3 80.6 - - - +
66H ARG* 1.3 65.5 + - - +
67H HIS* 2.9 21.7 + - - +
68H GLY* 2.8 24.2 + - - +
70H ILE* 5.8 1.1 - - + -
9I PHE* 3.7 18.8 - - + -
11I VAL* 3.8 19.3 - - + +
45I ILE* 4.6 4.5 - - + -
64I GLN* 4.6 1.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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