Contacts of the strand formed by residues 52 - 58 (chain B) in PDB entry 4GKH
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 LEU 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ASP 4.9 1.8 - - - +
23B LEU* 5.0 0.7 - - + -
26B TYR* 3.5 29.2 - - + +
42B ARG* 3.8 3.6 - - - +
43B LEU* 2.9 41.3 + - + +
50B PRO* 3.6 17.3 - - + +
51B GLU* 1.3 84.3 - - - +
53B PHE* 1.3 69.6 + - - +
85B LYS* 4.2 28.0 - - + +
97B LEU* 4.0 27.1 - - + -
98B THR 3.3 7.4 - - - +
99B THR* 3.8 26.9 - - + -
100B ALA 4.1 0.4 - - - +
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASP* 5.1 4.9 - - + -
40B ILE* 3.9 20.6 - - + -
41B TYR 3.4 13.2 - - - -
42B ARG* 3.4 50.0 - - + -
51B GLU* 4.8 0.7 - - - -
52B LEU* 1.3 75.5 - - - +
54B LEU* 1.3 60.5 + - - +
55B LYS* 4.2 4.3 - - + -
96B LEU 3.5 1.2 - - - +
97B LEU* 3.4 5.8 - - - +
98B THR* 2.8 44.3 + - - +
99B THR 5.1 1.1 - - - -
100B ALA* 3.7 32.5 - - + -
101B ILE 5.3 1.6 - - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 4.3 13.9 - - + -
23B LEU* 4.3 9.6 - - + -
28B TRP* 3.8 30.3 - - + -
39B THR 3.6 1.4 - - - +
40B ILE* 3.5 3.4 - - - -
41B TYR* 2.8 44.5 + - + +
43B LEU* 4.1 10.5 - - + -
53B PHE* 1.3 75.2 - - - +
55B LYS* 1.3 61.2 + - - +
95B TRP* 3.8 39.3 - - + -
96B LEU 3.3 24.2 - - - +
97B LEU* 4.0 19.5 - - + -
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Residues in contact with LYS 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 4.4 14.8 - - + +
39B THR 3.5 3.1 - - - -
40B ILE* 3.7 35.5 - - + +
53B PHE* 5.8 4.7 - - + -
54B LEU* 1.3 75.9 - - - +
56B HIS* 1.3 60.7 + - - +
57B GLY 4.2 0.4 - - - -
65B VAL* 4.4 10.3 - - + +
68B GLU* 2.5 37.4 + - - +
94B ALA 3.6 1.0 - - - +
95B TRP* 3.3 5.2 - - - +
96B LEU* 2.8 54.6 + - + +
216B ASP* 4.2 16.2 + - - +
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 3.5 5.4 - - - -
39B THR* 2.9 47.1 + - - +
41B TYR* 4.6 6.6 + - + -
54B LEU 4.1 0.2 + - - -
55B LYS* 1.3 74.0 - - - +
57B GLY* 1.3 67.1 + - - +
58B LYS* 4.4 14.2 + - + -
93B ASP* 2.8 27.3 + - - -
94B ALA 3.3 8.1 - - - -
95B TRP* 3.3 58.0 - + + -
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B HIS* 1.3 79.2 - - - +
58B LYS* 1.3 59.6 + - - -
61B VAL* 3.7 21.1 - - - -
62B ALA* 3.5 8.6 - - - +
65B VAL* 3.8 12.8 - - - +
93B ASP* 3.4 4.7 - - - -
94B ALA 2.9 34.1 + - - +
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B HIS* 4.4 11.2 + - + +
57B GLY* 1.3 73.9 - - - +
59B GLY* 1.3 70.7 + - - +
60B SER 3.3 0.5 + - - -
61B VAL* 3.0 22.4 + - - +
62B ALA 3.7 0.2 - - - +
92B ASP* 3.3 19.3 - - + +
93B ASP* 3.8 15.0 - - - +
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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