Contacts of the strand formed by residues 88 - 95 (chain I) in PDB entry 4DKE
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38I ARG* 4.3 8.3 - - + -
39I GLN 3.4 27.6 - - - +
40I ALA* 3.6 5.8 - - + +
41I PRO* 4.2 5.2 - - - -
85I GLU 5.4 0.2 - - - +
86I ASP 3.2 9.7 + - - +
87I THR* 1.3 80.5 - - - +
89I VAL* 1.3 64.9 + - - +
90I TYR* 3.3 16.1 - - + -
108I LEU* 4.1 5.6 - - - -
109I VAL 3.0 28.8 + - - -
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Residues in contact with VAL 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I VAL 4.1 0.5 - - - +
38I ARG* 3.3 2.6 - - - -
39I GLN* 2.8 41.5 + - + +
41I PRO* 5.5 0.4 - - - +
88I ALA* 1.3 73.8 - - - +
90I TYR* 1.3 62.1 + - - +
91I TYR* 3.5 35.5 - - + +
105I GLN 5.4 0.2 - - - +
106I GLY* 3.9 3.8 - - - -
107I THR 3.3 20.4 - - - +
108I LEU* 4.2 22.2 - - + +
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Residues in contact with TYR 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLU* 2.6 24.2 - - - +
20I LEU* 3.8 27.4 - - + -
36I TRP* 4.5 7.9 - + + -
37I VAL 3.7 2.9 - - - -
38I ARG* 3.3 40.9 + - + -
48I VAL* 4.9 4.5 - - + -
67I PHE* 4.0 12.9 - + - -
80I LEU* 4.1 9.9 - - + -
82I MET* 3.8 20.0 + - + -
86I ASP* 2.7 35.1 + - - +
88I ALA* 3.3 22.4 - - + -
89I VAL* 1.3 75.6 - - - +
91I TYR* 1.3 56.6 + - - +
106I GLY* 3.2 0.7 - - - -
107I THR* 2.8 25.7 + - + +
109I VAL* 3.8 21.4 - - + +
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Residues in contact with TYR 91 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLU* 3.6 2.5 - - - -
36I TRP* 3.2 11.0 - - - -
37I VAL* 2.7 51.3 + - + +
38I ARG* 5.0 0.4 - - - -
39I GLN* 3.8 20.5 + - + -
45I LEU* 4.6 5.8 - - + -
89I VAL* 3.5 27.9 - - + +
90I TYR* 1.3 73.9 - - - +
92I CYS* 1.3 60.0 + - - +
103I TRP* 3.7 30.3 - + + -
104I GLY 3.6 9.6 - - - -
105I GLN 4.0 3.4 - - - -
106I GLY* 3.4 27.8 - - - -
38M GLN* 3.6 14.8 + - - -
41M GLY 5.0 3.6 + - - -
42M LYS 3.7 7.5 + - - -
43M ALA* 3.6 23.3 - - + -
44M PRO* 4.1 9.6 - - + -
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Residues in contact with CYS 92 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 3.9 9.6 - - - +
6I GLU* 3.2 27.5 + - - -
22I CYS* 2.0 54.3 - - + -
34I ILE* 5.0 4.3 - - + -
35I HIS 3.2 10.5 - - - +
36I TRP* 3.6 16.2 - - + -
91I TYR* 1.3 74.4 - - - +
93I ALA* 1.3 61.4 + - - +
103I TRP* 3.6 0.5 - - - -
104I GLY* 2.7 29.5 + - - -
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Residues in contact with ALA 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.7 4.9 - - - +
34I ILE* 3.5 7.0 - - - +
35I HIS* 2.7 40.6 + - + +
37I VAL* 5.1 2.0 - - + -
91I TYR 4.2 0.2 - - - -
92I CYS* 1.3 77.1 - - - +
94I ARG* 1.3 60.3 + - - +
100I MET* 3.7 33.4 - - - +
102I TYR 3.2 12.6 - - - +
103I TRP* 4.0 17.3 - - + -
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Residues in contact with ARG 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 4.8 4.7 - - + +
27I PHE* 3.2 48.9 - - + +
29I PHE* 6.3 0.4 - - + -
32I THR* 3.9 21.8 - - - +
33I TRP 3.7 8.7 - - - +
34I ILE* 4.7 3.6 - - + +
35I HIS* 4.3 0.7 - - - -
93I ALA* 1.3 71.7 - - - +
95I GLY* 1.3 68.2 + - - +
96I LEU* 4.7 9.0 + - - -
100I MET* 3.3 4.0 - - - -
101I ASP* 2.6 63.0 + - - +
102I TYR* 3.0 43.8 + - + +
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Residues in contact with GLY 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I THR* 4.2 11.1 - - - +
33I TRP* 3.0 19.7 + - - +
35I HIS* 3.6 11.5 - - - -
94I ARG* 1.3 82.1 + - - +
96I LEU* 1.3 63.5 + - - -
97I GLY 3.4 4.7 + - - +
100I ARG* 3.3 31.9 - - - -
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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