Contacts of the strand formed by residues 55 - 64 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ASP* 3.5 8.9 - - + +
7C HIS* 3.2 28.8 + - + +
50C VAL 3.5 0.2 - - - +
51C GLU* 3.3 2.9 - - - -
52C ILE 2.9 37.2 + - - +
53C ASN* 4.3 5.2 - - + +
54C GLY* 1.3 81.2 - - - +
56C LYS* 1.3 62.7 + - - +
57C VAL* 3.4 7.9 + - + +
169C LEU* 3.9 10.4 - - + +
173C LYS* 2.5 36.4 + - - -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASP 4.2 6.3 - - - +
5C TYR* 3.6 21.6 - - + -
6C ASP* 2.6 44.5 + - - +
7C HIS 3.1 6.9 + - - -
49C THR* 5.1 6.1 - - + -
50C VAL 3.8 4.3 - - - -
51C GLU* 4.4 7.4 - - + +
54C GLY 3.9 1.8 + - - -
55C GLU* 1.3 68.9 - - - +
57C VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C TYR* 4.6 0.2 - - - -
7C HIS* 3.4 9.9 - - + +
9C PHE* 3.6 31.6 - - + -
48C ARG 3.9 0.5 - - - +
49C THR* 3.3 6.9 - - - +
50C VAL* 2.7 46.9 + - + +
52C ILE* 4.6 13.0 - - + -
55C GLU* 3.7 13.7 - - + +
56C LYS* 1.3 77.9 - - - +
58C LYS* 1.3 62.8 + - - +
59C LEU* 3.8 18.5 + - + +
165C THR* 4.4 6.5 - - + -
169C LEU* 4.1 23.3 - - + -
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Residues in contact with LYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A SO4 4.5 10.6 + - - -
4C ASP* 5.2 8.1 + - - +
5C TYR* 3.8 38.1 - - + +
7C HIS 2.7 14.4 + - - +
8C LEU* 3.3 21.5 - - + +
9C PHE 2.9 25.5 + - - -
47C ILE* 3.8 31.4 - - + +
48C ARG 3.5 4.5 - - - +
49C THR* 3.8 16.8 - - - +
56C LYS 4.2 0.2 + - - -
57C VAL* 1.3 75.0 - - - +
59C LEU* 1.3 66.8 + - - +
60C GLN* 5.2 1.3 - - - +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PHE* 3.4 37.9 - - + +
11C LEU* 4.4 17.3 - - + -
28C PHE* 3.6 19.8 - - + -
46C LYS 3.8 0.2 - - - +
47C ILE* 3.3 9.1 - - - +
48C ARG* 2.8 53.6 + - - +
50C VAL* 4.2 10.3 - - + -
57C VAL* 3.8 17.9 - - + +
58C LYS* 1.3 80.1 - - - +
60C GLN* 1.3 61.9 + - - +
165C THR* 4.1 28.7 - - + +
168C VAL* 4.7 3.6 - - + -
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Residues in contact with GLN 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A CYS* 4.7 6.7 - - - +
402A SO4 3.6 29.5 + - - -
8C LEU* 4.2 27.5 - - + +
9C PHE 2.9 10.3 + - - +
10C LYS* 3.8 25.9 + - - +
11C LEU* 2.7 36.7 + - - +
45C PHE* 5.3 0.9 - - + -
46C LYS 3.6 4.9 - - - +
47C ILE* 3.5 19.7 - - + -
58C LYS* 4.3 1.6 - - - +
59C LEU* 1.3 74.1 - - - +
61C ILE* 1.3 55.1 + - - +
62C TRP* 2.9 32.8 + - + +
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Residues in contact with ILE 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.3 16.8 - - + +
13C ILE* 3.8 22.4 - - + +
25C LEU* 3.5 43.2 - - + +
28C PHE* 3.4 30.0 - - + -
44C ASP 3.8 0.5 - - - +
45C PHE* 3.1 4.9 - - - -
46C LYS* 2.9 38.1 + - + +
59C LEU 4.2 0.2 + - - -
60C GLN* 1.3 74.6 - - - +
62C TRP* 1.3 65.6 + - - +
85C ILE* 3.7 30.5 - - + -
161C PHE* 4.6 5.8 - - + -
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Residues in contact with TRP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ASP 3.8 11.7 - - - -
238A TYR* 3.6 22.0 - + - -
240A CYS* 3.7 14.4 - - + -
241A ALA* 3.4 32.3 - - + -
242A PRO* 3.6 23.5 - - + +
243A MET* 3.6 17.5 - - + -
402A SO4 4.1 7.6 - - - -
10C LYS* 5.0 1.1 - - + +
11C LEU 2.9 21.5 + - - +
12C LEU* 3.5 9.8 - - + +
13C ILE* 3.0 26.3 + - - +
43C VAL* 3.8 17.5 - - + -
44C ASP 3.4 3.4 - - - -
45C PHE* 3.5 35.2 - + + -
60C GLN* 2.9 37.7 + - + +
61C ILE* 1.3 77.8 - - - +
63C ASP* 1.3 60.8 + - - +
77C TYR* 5.0 0.5 + - - -
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Residues in contact with ASP 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 3.4 22.0 - - + +
21C LYS* 2.8 50.2 + - - +
22C SER* 4.7 3.5 + - - -
25C LEU* 4.6 9.0 - - + +
38C ILE* 3.9 18.5 - - + +
43C VAL* 3.3 6.1 - - - +
44C ASP* 2.9 33.5 + - + +
62C TRP* 1.3 73.5 - - - +
64C THR* 1.3 76.3 + - - +
67C GLN* 3.3 5.2 + - - -
77C TYR* 4.5 0.9 - - - -
204C GDP 4.7 2.9 + - - -
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Residues in contact with THR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A HIS* 5.3 4.7 + - - +
226A VAL* 4.1 8.7 - - + +
243A MET* 3.7 24.5 - - - -
21C LYS* 3.6 5.5 + - - -
38C ILE* 3.5 8.1 - - - +
42C GLY 3.2 13.9 - - - +
43C VAL* 4.0 6.1 - - + -
63C ASP* 1.3 91.7 + - - +
65C ALA* 1.3 67.5 + - - +
67C GLN* 3.1 26.3 + - - +
70C PHE* 5.1 3.6 - - - -
77C TYR* 2.9 33.2 + - + +
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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