Contacts of the strand formed by residues 86 - 91 (chain D) in PDB entry 4QRR
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 SER 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ASN* 5.3 4.2 + - - +
23D CYS 3.4 12.9 + - - -
24D LEU* 3.9 15.4 - - - +
25D TYR* 4.0 3.1 - - - -
80D PHE* 4.4 0.5 - - - -
81D LYS* 2.9 64.0 + - - +
84D ALA* 4.2 10.1 - - - -
85D LYS* 1.3 78.0 - - - +
87D VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D CYS* 2.9 51.5 + - + +
25D TYR* 3.9 18.6 - - + -
39D ILE* 3.8 33.2 - - + -
41D TRP* 3.7 11.1 - - - +
56D GLN* 4.8 4.0 - - + -
78D VAL* 4.6 11.4 - - + -
79D ASN 3.5 11.0 - - - +
80D PHE* 4.3 21.1 - - + -
86D SER* 1.3 77.7 + - - +
88D ALA* 1.3 62.3 + - - +
104D CYS* 4.4 1.1 - - - -
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D THR* 3.8 16.4 - - + -
21D LEU 3.3 11.2 - - - +
22D ASN* 3.7 23.1 - - - +
41D TRP* 4.4 0.4 - - - -
77D SER 3.9 0.7 - - - +
78D VAL* 3.3 5.8 - - - -
79D ASN* 2.8 40.6 + - + +
81D LYS* 3.7 16.4 - - - +
86D SER* 5.5 0.2 - - - +
87D VAL* 1.3 74.8 - - - +
89D LEU* 1.3 61.0 + - - +
90D THR* 4.2 1.6 + - - -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL 3.7 0.9 - - - +
20D THR* 3.4 1.2 - - - -
21D LEU* 2.8 59.9 + - + +
41D TRP* 3.6 42.4 - - + -
53D LEU* 4.2 8.7 - - + -
54D ILE* 4.1 10.3 - - + -
76D TYR* 4.1 30.5 - - + -
77D SER 4.4 1.8 - - - +
78D VAL* 3.8 20.0 - - + -
88D ALA* 1.3 71.8 - - - +
90D THR* 1.3 63.7 + - - +
91D ILE* 4.2 11.2 + - + -
102D TYR* 3.9 15.5 - - + -
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Residues in contact with THR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 4.7 11.0 - - + -
19D VAL 3.2 14.4 - - - +
20D THR* 3.4 26.6 - - - +
75D ARG 3.2 5.5 - - - +
76D TYR* 3.6 0.9 - - - -
77D SER* 2.7 45.3 + - - -
79D ASN* 5.4 4.0 + - - +
88D ALA 4.2 3.1 + - - -
89D LEU* 1.3 75.4 - - - +
91D ILE* 1.3 65.5 + - - +
92D SER* 3.8 3.4 + - - +
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Residues in contact with ILE 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 3.3 4.0 - - - -
19D VAL* 3.1 32.8 + - + -
21D LEU* 3.8 22.0 - - + -
75D ARG* 3.4 32.3 - - + +
76D TYR* 3.7 26.2 - - + -
89D LEU* 4.2 5.8 - - + -
90D THR* 1.3 73.1 - - - +
92D SER* 1.3 59.4 + - - +
94D LEU* 3.9 11.9 - - + +
98D ASP* 3.9 15.3 - - - +
102D TYR* 3.7 34.8 - - + +
128D LEU* 4.0 13.2 - - + -
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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