Contacts of the strand formed by residues 52 - 58 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.8 2.7 - - + -
26D TYR* 3.3 36.1 - - + +
42D ARG* 3.5 6.2 - - - +
43D LEU* 2.7 52.4 + - + +
50D PRO* 3.7 9.0 - - + +
51D GLU* 1.3 83.6 - - - +
53D PHE* 1.3 65.1 + - - +
85D LYS* 4.0 13.5 - - + -
97D LEU* 4.0 25.8 - - + -
98D THR 3.4 14.6 - - - +
99D THR* 3.7 22.0 - - + -
100D ALA 4.3 0.7 - - - +
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Residues in contact with PHE 53 (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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31D ASP* 3.8 14.6 - - + -
40D ILE* 4.1 17.3 - - + -
41D TYR 3.3 13.7 - - - -
42D ARG* 3.6 29.2 - - + -
43D LEU* 4.2 1.8 - - - -
51D GLU* 4.4 3.8 - - - -
52D LEU* 1.3 74.4 - - - +
54D LEU* 1.3 60.2 + - - +
55D LYS* 6.2 2.0 - - + -
96D LEU 3.5 2.1 - - - +
97D LEU* 3.4 3.5 - - - +
98D THR* 2.8 47.5 + - - +
99D THR 4.8 1.6 - - - -
100D ALA* 3.6 34.3 - - + -
101D ILE 5.3 2.9 - - - -
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Residues in contact with LEU 54 (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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15C LEU* 5.6 1.8 - - + -
19D LEU* 4.6 15.3 - - + -
23D LEU* 5.4 0.9 - - + -
28D TRP* 3.6 31.0 - - + -
39D THR 3.4 1.4 - - - +
40D ILE* 3.3 6.0 - - - +
41D TYR* 2.8 49.8 + - + -
43D LEU* 3.9 14.1 - - + +
53D PHE* 1.3 73.7 - - - +
55D LYS* 1.3 61.8 + - - +
95D TRP* 3.9 40.8 - - + -
96D LEU 3.6 25.1 - - - +
97D LEU* 4.1 15.0 - - + +
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Residues in contact with LYS 55 (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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38D ALA* 4.2 20.6 - - + -
39D THR 3.3 2.2 - - - -
40D ILE* 4.2 28.0 - - + -
53D PHE* 4.1 2.2 - - + -
54D LEU* 1.3 76.5 - - - +
56D HIS* 1.3 61.1 + - - +
57D GLY 4.1 0.2 - - - -
65D VAL* 4.3 11.4 - - + +
68D GLU* 2.8 32.4 + - - +
94D ALA 3.6 1.0 - - - +
95D TRP* 3.3 5.5 - - - -
96D LEU* 2.8 53.0 + - + +
216D ASP* 2.9 27.1 + - - +
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Residues in contact with HIS 56 (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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14C ARG* 5.1 5.8 - - - -
38D ALA* 3.3 5.0 - - - +
39D THR* 2.8 52.9 + - - +
41D TYR* 4.6 6.4 + - + -
54D LEU 4.1 0.6 + - - -
55D LYS* 1.3 72.4 - - - +
57D GLY* 1.3 70.5 + - - +
58D LYS* 4.2 18.5 + - + -
93D ASP* 2.6 30.4 + - + -
94D ALA 3.3 12.3 - - - -
95D TRP* 3.4 50.5 - + + -
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Residues in contact with GLY 57 (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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56D HIS* 1.3 77.2 - - - +
58D LYS* 1.3 60.9 + - - -
61D VAL* 3.7 24.0 - - - -
62D ALA* 3.3 13.4 - - - +
65D VAL* 3.9 8.6 - - - +
93D ASP* 3.4 3.1 - - - -
94D ALA 2.9 34.4 + - - +
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Residues in contact with LYS 58 (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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14C ARG* 5.4 11.6 - - - +
16C ASN* 5.9 0.6 - - - +
56D HIS* 4.2 14.9 + - + +
57D GLY* 1.3 75.7 - - - +
59D GLY* 1.3 70.4 + - - +
60D SER 3.4 0.9 + - - -
61D VAL* 3.1 21.5 + - - +
62D ALA 3.8 0.2 - - - -
92D ASP* 3.4 13.8 - - + +
93D ASP* 2.7 37.7 + - - +
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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