Contacts of the strand formed by residues 88 - 94 (chain D) in PDB entry 1F11
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 ALA 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D LYS* 4.1 22.0 - - + -
39D GLN 3.1 20.4 - - - +
40D SER* 3.9 11.4 - - - +
41D HIS* 5.2 6.3 - - - +
86D ASP 3.4 3.8 + - - -
87D SER* 1.3 77.7 - - - +
89D VAL* 1.3 66.3 + - - +
90D TYR* 3.6 9.7 - - + +
107D THR 3.5 0.9 - - - +
108D LEU* 3.7 5.9 - - - +
109D VAL 3.0 29.7 + - - +
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Residues in contact with VAL 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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37D VAL 3.9 0.3 - - - +
38D LYS* 3.2 3.1 - - - +
39D GLN* 2.7 48.4 + - + +
88D ALA* 1.3 73.9 - - - +
90D TYR* 1.3 64.9 + - - +
91D TYR* 3.5 36.1 + - + +
106D GLY* 3.9 4.0 - - - -
107D THR 3.3 21.8 - - - +
108D LEU* 3.5 31.6 - - + -
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Residues in contact with TYR 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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6D GLN* 2.9 20.9 + - - +
20D MET* 3.7 22.2 - - + -
36D TRP* 5.1 0.4 - - + -
37D VAL 3.3 4.0 - - - +
38D LYS* 3.6 40.8 - - + +
48D ILE* 3.7 6.5 - - + -
63D PHE* 5.6 1.6 - + - -
80D MET* 3.3 31.9 - - + -
82D LEU* 3.6 24.5 - - + +
86D ASP* 2.6 40.6 + - - +
88D ALA* 3.6 22.6 - - + +
89D VAL* 1.3 73.9 - - - +
91D TYR* 1.3 62.1 + - - +
107D THR 3.0 23.3 + - - +
109D VAL* 3.9 10.3 - - + -
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Residues in contact with TYR 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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38C GLN* 3.8 0.2 + - - -
41C GLY 5.8 0.3 - - - -
42C GLN* 3.8 15.2 + - - -
43C PRO* 3.3 30.7 - - + -
44C PRO* 4.5 4.0 - - + -
6D GLN* 3.2 4.9 - - - +
36D TRP* 3.3 10.6 - - - -
37D VAL* 2.7 39.4 + - + +
39D GLN* 3.4 34.9 + - + -
45D LEU* 4.7 1.8 - - + -
89D VAL* 3.5 25.1 - - + +
90D TYR* 1.3 76.3 - - - +
92D CYS* 1.3 61.4 + - - +
103D TRP* 3.5 30.5 - + + -
104D GLY 3.5 17.9 - - - -
105D GLN 4.0 3.6 - - - -
106D GLY* 3.6 20.0 - - - -
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Residues in contact with CYS 92 (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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4D LEU* 4.1 9.8 - - - +
6D GLN* 3.1 24.0 + - - -
22D CYS* 2.0 53.4 - - + -
34D MET* 4.5 3.6 - - - -
35D LYS 3.1 10.1 - - - +
36D TRP* 3.7 18.2 - - + -
91D TYR* 1.3 75.5 - - - +
93D ALA* 1.3 61.3 + - - +
103D TRP* 3.5 1.7 - - - +
104D GLY* 2.9 25.6 + - - -
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Residues in contact with ALA 93 (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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4D LEU* 4.1 3.1 - - - -
34D MET* 3.4 9.3 - - - +
35D LYS* 2.7 32.0 + - + +
37D VAL* 5.2 1.6 - - + -
92D CYS* 1.3 75.5 - - - +
94D ASN* 1.3 65.6 + - - +
100D PHE* 3.9 32.1 - - - +
102D TYR 3.0 17.9 - - - +
103D TRP* 4.2 13.5 - - + -
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Residues in contact with ASN 94 (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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2D VAL* 3.8 10.1 - - - +
4D LEU* 4.4 5.7 - - - +
27D TYR* 3.2 45.2 + - - +
32D TYR* 4.9 3.5 - - + +
33D TYR 3.6 17.3 - - - +
34D MET* 4.5 4.5 - - - -
35D LYS* 4.5 8.1 - - - -
93D ALA* 1.3 79.1 - - - +
95D ASP* 1.3 58.8 + - - +
96D TYR* 3.5 15.2 + - - +
100D GLY 3.9 0.8 - - - +
101D ALA 3.1 21.8 + - - -
102D TYR* 3.0 29.6 + - - +
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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