Contacts of the strand formed by residues 87 - 90 (chain K) in PDB entry 6D6Q
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 ASN 87 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48K LEU* 3.2 34.2 - - - +
49K GLU* 3.6 24.2 - - + +
52K PRO* 5.0 4.5 - - + -
64K HIS 5.0 2.7 - - - +
65K TYR* 2.9 40.9 - - + -
66K LEU* 3.1 21.8 - - - +
85K ILE* 4.1 6.0 - - - +
86K ARG* 1.3 79.8 + - + +
88K VAL* 1.3 82.8 + - - +
119K HIS* 3.4 16.4 - - + +
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Residues in contact with VAL 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K TYR* 5.7 0.2 - - - +
66K LEU* 3.1 33.7 - - + +
68K PRO* 3.9 14.4 - - + -
80K LEU* 5.2 11.4 - - + -
85K ILE* 5.0 2.2 - - + -
87K ASN* 1.3 88.1 + - - +
89K ILE* 1.3 77.6 + - - +
90K VAL* 4.8 4.0 - - + -
119K HIS 2.6 21.3 + - - +
120K PHE* 3.0 47.6 - - + -
121K TYR* 3.6 10.4 + - - +
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Residues in contact with ILE 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K CYS 5.2 0.2 - - - +
48K LEU* 4.0 25.8 - - + -
65K TYR* 4.6 8.5 - - + -
66K LEU 2.6 14.3 + - - +
67K LEU* 3.5 14.2 - - + +
68K PRO* 3.4 15.2 - - - +
88K VAL* 1.3 90.3 - - - +
90K VAL* 1.3 76.7 + - - +
91K LEU* 4.8 4.3 - - + -
121K TYR* 3.7 7.4 - - + +
123K PHE* 4.5 6.3 - - + -
156K TYR* 3.2 56.5 - - + +
171K VAL* 4.2 18.8 - - + -
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Residues in contact with VAL 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K LEU* 5.5 0.2 - - - -
68K PRO* 5.2 7.6 - - + -
73K LEU* 5.9 8.1 - - + -
88K VAL* 4.8 5.4 - - + -
89K ILE* 1.3 86.2 - - - +
91K LEU* 1.3 77.5 + - - +
94K VAL* 5.3 7.2 - - + -
95K LEU* 4.7 13.9 - - + +
109K ILE* 5.1 17.0 - - + -
113K THR* 5.4 1.3 - - + -
120K PHE* 4.4 29.4 - - + +
121K TYR 2.9 11.5 + - - +
122K THR* 4.4 13.7 - - + +
123K PHE* 2.9 25.5 + - - +
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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