Contacts of the strand formed by residues 91 - 97 (chain H) in PDB entry 3KJ4
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 91 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.3 35.4 - - + +
39H GLN 3.2 18.4 - - - +
40H SER* 3.8 9.6 - - - +
41H PRO* 4.5 0.9 - - - -
88H ASP 5.6 0.2 - - - +
89H ASP* 3.4 2.9 + - - -
90H THR* 1.3 76.6 - - - +
92H ILE* 1.3 63.3 + - - +
93H TYR* 3.6 5.5 - - + -
115H LEU* 3.5 4.7 - - - +
116H VAL* 2.8 32.7 + - - +
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Residues in contact with ILE 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H ARG* 3.5 4.5 - - - +
39H GLN* 2.6 40.5 + - - +
40H SER 4.4 10.1 - - - +
41H PRO* 5.6 3.6 - - + -
91H ALA* 1.3 77.0 - - - +
93H TYR* 1.3 65.6 + - - +
94H TYR* 3.9 31.3 + - + +
112H GLN 4.6 0.7 - - - +
113H GLY* 3.5 35.0 - - - +
114H THR 3.8 5.6 - - - +
115H LEU* 4.0 22.7 - - + +
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Residues in contact with TYR 93 (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 GLU* 3.6 10.0 - - - +
18H LEU* 4.3 14.8 - - + -
20H ILE* 3.7 28.5 - - + -
36H TRP* 3.8 6.0 - + + -
37H VAL 3.9 2.0 - - - -
38H ARG* 3.0 34.5 + - + -
48H LEU* 3.7 23.1 - - + -
80H LEU* 4.2 5.8 - - + -
82H MET* 4.2 9.5 - - - -
85H LEU* 4.7 1.6 - - - +
89H ASP* 2.7 34.5 + - - +
91H ALA* 3.6 16.8 - - + -
92H ILE* 1.3 78.3 - - - +
94H TYR* 1.3 63.1 + - - +
114H THR* 2.9 34.0 + - + +
116H VAL* 3.7 24.5 - - + -
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Residues in contact with TYR 94 (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 GLU* 3.3 7.0 - - - +
36H TRP* 3.2 9.1 - - - -
37H VAL 2.8 39.5 + - - +
39H GLN* 3.1 40.3 + - + -
45H LEU* 4.1 9.4 - - + -
92H ILE* 4.0 25.8 - - + +
93H TYR* 1.3 72.5 - - - +
95H CYS* 1.3 60.1 + - - +
110H TRP* 3.6 31.2 - + + -
111H GLY 4.0 5.4 - - - +
112H GLN 3.2 22.6 + - - -
113H GLY* 3.5 16.8 - - - -
44L GLN* 3.2 14.7 + - - -
48L GLN 4.6 1.9 + - - -
49L SER* 3.5 21.2 + - - -
50L PRO* 4.2 2.2 - - + -
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Residues in contact with CYS 95 (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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4H LEU* 3.6 12.8 - - - +
6H GLU* 2.9 25.5 + - - +
22H CYS* 2.1 48.9 - - - -
34H VAL* 4.3 0.9 - - + -
35H HIS 3.4 14.6 - - - +
36H TRP* 3.5 17.5 - - + -
94H TYR* 1.3 74.1 - - - +
96H ALA* 1.3 59.7 + - - +
110H TRP 3.5 1.6 - - - -
111H GLY 3.0 23.1 + - - -
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Residues in contact with ALA 96 (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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4H LEU* 4.1 4.9 - - - -
34H VAL* 3.5 4.9 - - - +
35H HIS* 2.9 30.4 + - + -
37H VAL* 4.6 3.1 - - + +
94H TYR 4.1 0.6 + - - -
95H CYS* 1.3 73.4 - - - +
97H ARG* 1.3 65.7 + - - +
107H PHE* 3.7 24.2 - - + -
109H TYR 3.1 16.8 - - - +
110H TRP* 3.8 27.4 - - + -
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Residues in contact with ARG 97 (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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2H VAL* 3.9 8.1 - - - +
4H LEU* 4.1 12.3 - - + +
27H PHE* 3.2 62.2 - - + +
32H TYR* 3.6 39.9 + - - -
33H GLY 4.0 9.6 - - - +
34H VAL* 4.7 3.1 - - - -
35H HIS* 4.6 2.9 - - - -
96H ALA* 1.3 79.7 - - - +
98H VAL* 1.3 106.1 - - + +
104H GLY 5.2 3.6 + - - -
107H PHE* 3.5 17.0 - - - -
108H ALA 3.6 2.6 + - - -
109H TYR* 2.9 49.8 + - + +
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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