Contacts of the strand formed by residues 71 - 76 (chain H) in PDB entry 2QXU
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 VAL 71 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ASN* 4.1 0.2 - - - -
5H PRO* 3.4 14.6 - - + +
7H VAL* 4.0 12.8 - - + -
59H VAL* 3.8 21.8 - - + -
62H VAL* 3.7 25.6 - - + -
63H LEU* 3.6 26.0 - - + -
70H LYS* 1.3 74.8 - - - +
72H ASP* 1.3 70.6 + - - +
73H ILE* 4.4 11.2 - - + -
95H LYS 2.9 15.8 + - - +
96H VAL* 3.4 7.8 - - + +
97H ALA 3.0 23.6 + - - -
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Residues in contact with ASP 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H HIS* 5.7 0.3 - - - -
4H ASN* 3.1 37.9 + - - +
5H PRO 2.9 10.1 + - - +
6H VAL* 3.5 9.0 - - + +
7H VAL* 2.8 26.7 + - - +
31H TRP* 5.5 1.4 + - - -
71H VAL* 1.3 73.4 - - - +
73H ILE* 1.3 65.9 + - - +
97H ALA* 3.3 1.6 - - - +
98H ASN* 2.9 47.6 + - - +
173H LEU* 3.6 28.5 - - + +
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Residues in contact with ILE 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H VAL* 3.3 19.7 - - + +
9H VAL* 3.8 9.2 - - + -
55H LEU* 4.9 7.2 - - + -
59H VAL* 5.0 4.7 - - + -
71H VAL* 4.4 8.1 - - + -
72H ASP* 1.3 81.2 - - - +
74H VAL* 1.3 72.5 + - - +
75H ALA* 4.1 2.5 - - + +
83H THR* 3.7 42.0 - - + +
86H TYR* 4.6 13.0 - - + -
96H VAL* 4.0 25.1 - - + -
98H ASN 2.8 12.2 + - - +
99H VAL* 3.4 6.8 - - + -
100H VAL* 2.8 33.3 + - - +
173H LEU* 4.7 1.2 - - - +
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Residues in contact with VAL 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H VAL* 4.0 19.1 - - + -
7H VAL 3.1 4.9 + - - +
8H MET* 3.2 17.8 - - + -
9H VAL 2.8 24.6 + - - -
19H PHE* 3.9 14.3 - - + -
22H ILE* 4.8 6.1 - - + -
26H LEU* 5.1 0.2 - - + -
73H ILE* 1.3 78.1 - - - +
75H ALA* 1.3 62.1 + - - +
100H VAL* 3.2 10.1 - - + +
102H LEU* 4.0 25.6 - - + -
169H ILE* 4.3 18.6 - - + -
173H LEU* 4.0 23.1 - - + -
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Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 3.4 8.1 - - + +
19H PHE* 4.7 1.1 - - - -
73H ILE* 4.0 2.9 - - + -
74H VAL* 1.3 75.8 - - - +
76H HIS* 1.3 54.7 + - - +
79H GLY 3.6 18.2 - - - +
80H GLY* 3.7 8.5 - - - +
83H THR* 3.6 24.0 - - - +
99H VAL* 5.8 0.4 - - + -
100H VAL 2.8 12.7 + - - +
101H THR* 3.2 7.2 - - + -
102H LEU* 2.6 37.7 + - - +
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Residues in contact with HIS 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL 2.9 11.2 + - - +
10H HIS* 4.7 0.7 - - - -
11H GLY* 3.5 16.3 + - - +
18H ASN* 5.2 6.0 + - + -
19H PHE* 4.2 9.6 - - + -
75H ALA* 1.3 74.9 - - - +
77H SER* 1.3 62.4 + - - +
78H MET 3.2 1.0 + - - -
79H GLY* 2.7 27.7 + - - -
102H LEU* 3.2 33.2 - - + -
156H HIS* 2.9 52.8 + + - -
157H ILE* 5.1 1.6 - - + -
159H LEU* 4.2 3.9 - - + +
160H LEU* 3.7 42.9 - - + +
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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