Contacts of the strand formed by residues 84 - 89 (chain C) in PDB entry 5DQZ
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 ARG 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C VAL* 3.9 19.4 - - + +
78C VAL* 3.9 8.1 - - - -
83C VAL* 1.3 77.8 - - - +
85C VAL* 1.3 81.5 + - - +
86C TYR* 4.3 2.4 - - - +
87C ALA* 3.3 23.1 - - - +
185C SER* 3.1 23.1 + - - +
188C TYR* 5.0 17.3 - - + -
189C GLY* 5.8 1.3 - - - +
192C GLU* 3.0 39.2 + - - -
213C LEU* 3.6 37.9 - - - +
90D GLN* 5.8 2.8 - - - +
91D PRO* 5.4 2.0 - - - +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TRP* 2.7 18.6 + - + +
78C VAL 4.1 0.9 - - - -
79C GLY* 3.5 28.3 - - - +
83C VAL* 3.7 7.2 - - + +
84C ARG* 1.3 91.7 + - - +
86C TYR* 1.3 64.9 + - + +
62D HIS* 5.5 2.5 - - + -
65D VAL* 4.7 2.0 - - + -
66D ARG* 3.9 31.9 - - + +
69D ALA* 3.5 32.1 - - + +
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Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 3.5 6.2 - - - +
77C TRP* 2.9 36.4 + + + +
84C ARG* 4.2 6.7 - - - +
85C VAL* 1.3 77.8 - - + +
87C ALA* 1.3 77.6 + - - +
65D VAL* 3.3 32.3 - - + -
68D ALA* 4.6 1.1 - - + -
69D ALA* 3.8 29.2 - - + -
73D THR 3.0 28.0 + - - -
74D LEU* 3.6 3.5 - - - -
75D LEU* 3.0 36.8 + - + -
77D TRP* 4.9 2.7 - + - -
89D GLY* 3.6 26.8 - - - -
90D GLN* 4.1 20.3 - - + +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 4.3 7.6 - - + -
75C LEU 3.2 11.7 - - - +
76C VAL* 4.6 4.7 - - + -
77C TRP* 4.1 4.9 - - - -
84C ARG* 3.3 26.1 - - - +
86C TYR* 1.3 82.5 - - - +
88C SER* 1.3 60.2 + - - +
192C GLU* 3.8 17.0 - - - +
89D GLY* 3.1 23.6 - - - -
90D GLN 3.3 7.4 + - - +
91D PRO* 4.0 5.4 - - + -
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 3.4 24.3 + - - +
69C ALA* 5.8 0.2 - - - +
73C THR 4.3 0.9 - - - +
74C LEU* 3.2 9.9 - - - +
75C LEU* 2.9 38.7 + - - +
77C TRP* 3.5 26.2 - - - -
87C ALA* 1.3 74.9 - - - +
89C GLY* 1.3 60.6 + - - +
77D TRP* 4.0 10.5 - - - -
87D ALA* 3.9 7.3 - - - +
88D SER 3.5 8.9 + - - -
91D PRO* 4.4 1.1 - - - -
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Residues in contact with GLY 89 (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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69C ALA* 4.2 15.9 - - - -
73C THR 4.9 4.7 - - - -
74C LEU* 4.4 9.0 - - - -
88C SER* 1.3 78.6 + - - +
90C GLN* 1.3 70.0 + - - +
196C LEU* 5.7 1.1 - - - -
87D ALA* 3.7 1.3 - - - -
88D SER 3.1 26.8 + - - +
91D PRO* 4.2 5.5 - - - +
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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