Contacts of the strand formed by residues 74 - 78 (chain C) in PDB entry 6ATH
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 TYR 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 4.0 7.2 - - + -
22A ARG 3.6 0.7 - - - -
23A ASN* 3.1 48.7 + - + -
28A GLU* 4.7 0.7 - - + -
30A VAL* 4.1 27.5 - - + +
59C LYS 3.5 24.7 - - - -
60C TRP* 3.4 38.6 - + - -
61C ASN* 2.9 41.3 + - - +
70C LEU 4.3 1.4 - - - +
72C GLY 3.6 5.5 + - - +
73C LYS* 1.3 89.3 - - + +
75C GLU* 1.3 60.5 + - - +
76C TRP* 3.2 22.4 + + + +
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.2 17.3 - - - +
22A ARG* 3.3 22.8 + - + +
24A LYS* 4.1 28.5 - - + +
72C GLY 4.8 1.6 - - - +
74C TYR* 1.3 69.6 - - - +
76C TRP* 1.3 59.5 + - - +
77C GLN* 2.9 24.7 + - + +
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Residues in contact with TRP 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.6 33.2 - - + -
20A LYS* 3.3 9.0 - - - -
21A ALA* 3.6 18.8 - - + -
30A VAL* 4.2 17.9 - - + -
32A LEU* 3.8 36.3 - - + -
79A VAL* 5.3 2.9 - - + -
60C TRP* 2.9 42.7 + + + -
61C ASN* 3.2 19.9 + - - +
62C PHE* 3.7 24.6 - + + +
64C PHE* 6.1 0.7 - + - -
69C PRO* 3.7 24.2 - - + +
70C LEU 4.2 2.2 - - - -
74C TYR* 3.2 30.1 + + + +
75C GLU* 1.3 65.6 - - - +
77C GLN* 1.3 64.0 + - - +
78C GLU* 3.5 4.9 + - - +
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Residues in contact with GLN 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 3.7 1.1 - - - -
20A LYS* 2.9 65.1 + - + +
21A ALA 4.5 0.4 - - - -
22A ARG* 4.0 21.4 - - - +
29A VAL* 5.5 1.2 - - - +
75C GLU* 2.9 21.1 + - + +
76C TRP* 1.3 71.9 - - - +
78C GLU* 1.3 65.8 + - - +
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Residues in contact with GLU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL 4.0 4.9 - - - +
19A TYR* 3.5 37.8 + - + -
20A LYS* 5.3 2.3 - - - +
69C PRO* 5.8 0.2 - - + -
76C TRP 4.2 3.6 - - - +
77C GLN* 1.3 80.7 - - - +
79C VAL* 1.3 70.7 + - - +
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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