Contacts of the strand formed by residues 78 - 84 (chain Q) in PDB entry 5A31
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 78 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65Q THR* 3.8 12.8 - - + +
66Q ILE 3.4 6.7 - - - +
67Q HIS* 3.7 33.8 + - + +
76Q ASP 5.9 0.4 - - - +
77Q LEU* 1.3 77.7 - - - +
79Q TYR* 1.3 62.8 + - - +
80Q LYS* 2.8 47.7 - - - +
100Q THR* 4.0 3.1 + - - +
170Q TYR* 2.6 39.6 + - - +
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Residues in contact with TYR 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65Q THR* 3.3 6.6 - - - +
66Q ILE* 2.9 39.7 + - + +
68Q GLY 5.6 0.2 - - - -
74Q TYR* 3.5 32.1 - + + -
77Q LEU* 3.7 31.9 - - + +
78Q ARG* 1.3 77.1 - - - +
80Q LYS* 1.3 62.8 + - - +
81Q LEU* 3.7 3.6 - - + +
98Q PHE* 3.7 25.6 - + + -
100Q THR* 3.6 20.0 - - + -
101Q PRO 3.5 19.7 - - - -
102Q CYS* 3.7 29.1 - - + -
103Q TYR 4.7 0.5 + - - -
139Q LEU* 4.7 12.1 - - + -
166Q LEU* 3.8 6.2 - - - +
170Q TYR* 3.8 18.4 - + - -
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Residues in contact with LYS 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763N THR* 6.1 3.2 - - - +
764N ASN* 5.6 4.5 + - - -
63Q VAL* 3.7 20.4 - - + +
64Q GLY 3.2 5.4 - - - -
65Q THR* 3.1 24.7 - - - +
78Q ARG* 2.8 35.5 - - - +
79Q TYR* 1.3 74.0 - - - +
81Q LEU* 1.3 63.2 + - - +
98Q PHE* 3.8 2.6 - - - -
99Q LEU* 2.8 37.5 + - + -
100Q THR* 2.8 22.8 + - - +
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Residues in contact with LEU 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63Q VAL* 3.4 6.4 - - - +
64Q GLY* 2.9 38.0 + - - +
66Q ILE* 3.8 28.0 - - + -
79Q TYR 3.7 20.2 - - - +
80Q LYS* 1.3 76.8 - - - +
82Q SER* 1.3 64.1 + - - +
83Q LEU* 4.7 2.9 - - + -
96Q VAL* 4.1 10.3 - - + -
97Q LYS 3.2 12.6 - - - +
98Q PHE* 3.8 40.2 - - + -
99Q LEU* 3.7 9.7 - - - +
113Q ILE* 4.1 0.7 - - + -
132Q LEU* 5.1 3.8 - - + -
135Q ILE* 4.1 24.0 - - + -
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Residues in contact with SER 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Q LYS* 4.7 21.1 - - - -
62Q TRP 3.5 7.4 - - - -
63Q VAL* 5.8 0.4 - - - -
81Q LEU* 1.3 74.7 - - - +
83Q LEU* 1.3 63.6 + - - +
84Q GLU* 4.9 5.8 - - - -
95Q THR 3.6 1.3 + - - +
96Q VAL* 3.3 7.8 - - - +
97Q LYS* 2.9 45.8 + - - +
99Q LEU* 3.6 27.3 - - - +
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Residues in contact with LEU 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Q ALA* 4.8 2.7 - - + -
61Q LYS* 3.3 4.2 - - - +
62Q TRP* 2.9 47.1 + - + +
63Q VAL 4.0 1.8 - - - -
64Q GLY* 3.5 33.7 - - - +
81Q LEU* 4.0 5.4 - - + +
82Q SER* 1.3 79.0 - - - +
84Q GLU* 1.3 63.6 + - - +
85Q PHE* 3.9 24.8 - - + -
94Q PRO* 5.3 0.7 - - + -
95Q THR 3.4 5.2 - - - -
96Q VAL* 4.1 21.8 - - + -
128Q VAL* 4.2 25.8 - - + -
131Q ILE* 4.7 11.2 - - + -
132Q LEU* 4.6 11.9 - - + -
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Residues in contact with GLU 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Q PHE 3.6 4.0 - - - +
61Q LYS* 2.2 46.8 + - + +
82Q SER* 4.9 7.6 + - - -
83Q LEU* 1.3 78.6 - - - +
85Q PHE* 1.3 63.6 + - - +
86Q PRO* 3.8 1.8 - - - +
94Q PRO* 3.3 5.2 - - - +
95Q THR* 2.8 58.4 + - - +
97Q LYS* 4.9 8.9 + - - +
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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