Contacts of the strand formed by residues 55 - 64 (chain D) in PDB entry 6EKK
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 GLU 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D ASP* 3.5 18.2 - - + +
7D HIS* 2.9 34.7 + - + -
51D GLU* 3.2 6.2 - - - -
52D ILE 2.7 39.0 + - - +
53D ASN* 3.9 11.6 - - - +
54D GLY* 1.3 82.5 - - - +
56D LYS* 1.3 61.5 + - - +
57D VAL* 3.5 5.0 + - + +
169D LEU* 4.4 9.9 - - - +
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Residues in contact with LYS 56 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D ASP 4.5 7.0 - - - +
5D TYR* 3.8 10.6 - - + +
6D ASP* 2.7 49.9 + - - +
7D HIS 3.2 6.1 + - - +
50D VAL 4.0 2.9 - - - +
51D GLU* 3.4 18.9 + - - +
55D GLU* 1.3 69.6 - - - +
57D VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 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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5D TYR* 5.2 0.4 - - - -
7D HIS* 3.6 10.5 - - + +
9D PHE* 3.6 33.4 - - + -
48D ARG 3.6 1.4 - - - +
49D THR* 3.3 4.6 - - - -
50D VAL* 2.9 42.5 + - + +
52D ILE* 4.2 19.5 - - + +
55D GLU* 3.7 15.0 - - + +
56D LYS* 1.3 77.4 - - - +
58D LYS* 1.3 62.8 + - - +
59D LEU* 4.1 17.0 - - + -
165D THR* 4.8 4.7 - - + -
169D LEU* 4.2 20.0 - - + -
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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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5D TYR* 4.3 21.5 - - + +
7D HIS 2.8 15.6 + - - +
8D LEU* 3.3 21.5 - - + +
9D PHE 2.8 25.8 + - - -
47D ILE* 3.9 17.0 - - + -
48D ARG 3.5 2.2 - - - -
49D THR* 3.8 23.1 - - + -
56D LYS 4.1 0.2 + - - -
57D VAL* 1.3 74.2 - - - +
59D LEU* 1.3 65.0 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D PHE* 3.4 31.9 - - + +
11D LEU* 4.1 21.5 - - + -
28D PHE* 3.8 35.2 - - + -
46D LYS 3.8 0.2 - - - +
47D ILE* 3.2 8.2 - - - +
48D ARG 2.8 40.3 + - - +
50D VAL* 4.0 19.1 - - + -
57D VAL* 4.1 6.5 - - + -
58D LYS* 1.3 78.6 - - - +
60D GLN* 1.3 63.5 + - - +
61D ILE* 5.5 1.2 - - + +
165D THR* 4.1 30.1 - - + +
168D VAL* 4.6 3.4 - - + -
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Residues in contact with GLN 60 (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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240B CYS* 4.9 11.1 - - - +
8D LEU* 3.9 27.7 - - + +
9D PHE 2.8 10.4 + - - +
10D LYS* 3.2 27.7 + - + +
11D LEU* 2.6 36.5 + - - +
45D PHE* 5.1 1.9 - - + -
46D LYS 3.5 4.7 - - - +
47D ILE* 3.4 23.5 - - + +
59D LEU* 1.3 74.6 - - - +
61D ILE* 1.3 55.6 + - - +
62D TRP* 3.0 35.4 + - + +
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Residues in contact with ILE 61 (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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11D LEU* 3.5 34.1 - - + +
12D LEU 3.5 2.5 - - - +
13D ILE* 3.5 29.6 - - + +
25D LEU* 3.5 44.4 - - + +
28D PHE* 5.5 11.4 - - + -
29D ALA* 6.4 0.4 - - - -
44D ASP 3.8 0.5 - - - +
45D PHE* 3.1 4.2 - - - +
46D LYS* 2.8 55.5 + - + +
47D ILE* 5.4 1.3 - - - -
59D LEU* 5.5 1.8 - - + +
60D GLN* 1.3 73.7 - - - +
62D TRP* 1.3 60.5 + - - +
85D ILE* 4.3 12.3 - - + -
161D PHE* 5.6 0.9 - - + -
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Residues in contact with TRP 62 (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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237B ASP 4.0 10.8 - - - -
238B TYR* 3.6 23.1 - + - -
240B CYS* 3.6 9.6 - - + -
241B ALA* 3.3 41.5 - - + -
242B PRO* 3.6 24.6 - - + +
243B MET* 3.8 15.7 - - + -
10D LYS* 4.3 4.2 - - + +
11D LEU 2.8 20.0 + - - +
12D LEU* 3.5 11.1 - - + +
13D ILE* 3.0 25.3 + - - +
43D VAL* 3.9 13.9 - - + -
44D ASP 3.4 3.6 - - - -
45D PHE* 3.5 36.6 - + + -
60D GLN* 3.0 39.9 + - + +
61D ILE* 1.3 79.5 - - - +
63D ASP* 1.3 61.7 + - - +
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Residues in contact with ASP 63 (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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13D ILE* 3.3 27.0 - - + +
21D LYS* 2.8 51.5 + - - +
22D SER* 4.8 3.3 + - - -
25D LEU* 5.2 5.7 - - + +
38D ILE* 3.6 19.4 - - + +
43D VAL* 3.3 5.5 - - - +
44D ASP* 2.9 37.2 + - + +
62D TRP* 1.3 73.9 - - - +
64D THR* 1.3 73.9 + - - +
67D GLN* 3.3 1.7 + - - +
77D TYR* 4.5 1.1 - - - -
203D GDP 4.7 2.8 + - - -
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Residues in contact with THR 64 (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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225B HIS* 5.2 5.2 + - - +
226B VAL* 4.1 10.5 - - + +
243B MET* 3.8 26.5 - - + -
21D LYS* 3.8 4.0 + - - -
38D ILE* 3.5 9.5 - - - +
42D GLY 3.3 13.9 - - - +
43D VAL* 4.1 4.7 - - + -
63D ASP* 1.3 90.2 + - - +
65D ALA* 1.3 66.7 + - - +
66D GLY 3.9 0.2 + - - -
67D GLN* 3.0 23.4 + - - +
70D PHE* 5.1 3.3 - - - -
77D TYR* 2.8 32.0 + - + +
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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