Contacts of the strand formed by residues 14 - 19 (chain K) in PDB entry 2EHO
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 14 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12K LYS 3.5 6.7 + - - +
13K GLU* 1.3 81.1 + - - +
15K VAL* 1.3 69.6 + - - +
33K LEU* 6.0 1.1 - - + -
43K GLU* 3.7 28.5 - - + +
44K VAL* 3.3 19.5 - - - +
45K PRO* 3.9 13.7 - - + -
95K LEU* 5.2 0.7 - - - +
1007K SO4 3.4 23.8 + - - +
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Residues in contact with VAL 15 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K GLU 4.4 4.7 - - - +
14K LEU* 1.3 84.0 - - - +
16K THR* 1.3 81.4 + - - +
17K ILE* 4.6 2.0 - - + -
42K VAL 3.5 0.3 - - - +
43K GLU* 3.5 1.9 - - - -
44K VAL* 2.7 37.5 + - - +
46K LEU* 4.4 9.9 - - + -
49K ALA* 4.7 7.4 - - + -
60K LEU* 4.0 21.1 - - + -
61K LEU 4.2 10.8 - - - +
63K PRO* 4.9 10.3 - - + -
95K LEU* 4.1 23.8 - - + -
99K LEU* 5.0 11.2 - - + -
1007K SO4 3.2 14.4 - - - +
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Residues in contact with THR 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H VAL* 4.5 7.3 - - + +
15K VAL* 1.3 80.7 - - - +
17K ILE* 1.3 71.6 - - - +
41K PRO* 3.9 24.2 - - + -
42K VAL 3.3 8.4 + - - +
43K GLU* 3.3 12.6 + - - -
61K LEU* 3.2 58.5 + - + +
1007K SO4 2.8 24.4 + - - -
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Residues in contact with ILE 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K VAL* 4.6 3.6 - - + +
16K THR* 1.3 76.3 - - - +
18K ILE* 1.3 64.4 + - - +
19K PRO* 3.4 22.2 - - + +
36K PHE* 4.7 3.8 - - + -
41K PRO* 3.6 1.9 - - - +
42K VAL* 3.0 41.1 + - + +
44K VAL* 4.8 8.7 - - + -
49K ALA* 3.6 21.8 - - + -
52K LEU* 3.9 19.3 - - + -
58K CYS* 3.5 30.7 - - + -
59K ARG 3.0 9.4 - - - +
60K LEU* 3.3 30.3 - - + -
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Residues in contact with ILE 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H TRP* 4.0 18.6 - - + -
16K THR* 4.3 1.6 - - + -
17K ILE* 1.3 79.9 - - - +
19K PRO* 1.3 64.2 - - - +
20K ASN* 4.9 1.0 - - - +
39K GLY* 3.6 37.0 - - - +
40K LEU 4.2 0.2 - - - -
41K PRO* 4.2 9.9 - - + -
58K CYS* 3.3 2.1 - - - -
59K ARG* 2.7 63.4 + - + +
61K LEU* 3.0 48.0 - - + -
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Residues in contact with PRO 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K ILE* 3.4 15.2 - - + +
18K ILE* 1.3 88.1 - - + +
20K ASN* 1.3 59.2 + - - +
21K PHE* 3.3 34.1 - - + +
36K PHE* 4.1 11.2 - - + -
37K ASN 3.9 6.7 - - - +
38K PRO* 3.0 1.8 - - - +
39K GLY 2.8 26.5 + - - -
40K LEU 3.0 22.2 - - - +
42K VAL* 3.3 22.0 - - + -
57K LYS 3.5 8.7 - - - +
58K CYS* 3.7 2.4 - - + -
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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