Contacts of the strand formed by residues 52 - 58 (chain K) in PDB entry 5EEZ
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 THR 52 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101J TRP* 2.7 39.9 + - + +
23K GLY* 4.2 4.9 - - - -
24K LEU 3.3 5.8 - - - +
26K ARG* 3.6 1.6 + - - +
33K HIS* 2.9 18.4 + - - -
47K GLN 4.4 2.9 - - - +
48K PHE* 3.6 6.4 - - + -
49K THR* 2.9 34.7 + - - +
51K HIS* 1.3 76.9 - - - +
53K SER* 1.3 57.6 + - - +
54K ALA 3.5 21.1 - - - +
55K ILE* 3.9 17.7 - - + -
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Residues in contact with SER 53 (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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47A GLN* 3.0 36.7 + - - +
49A THR* 3.7 17.3 - - - -
24K LEU 3.2 4.1 + - - -
25K THR 3.5 1.4 + - - -
26K ARG* 3.4 33.1 - - - +
48K PHE* 3.9 6.1 - - - -
52K THR* 1.3 75.5 - - - +
54K ALA* 1.3 60.1 + - - +
101K TRP* 2.9 32.6 + - - +
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Residues in contact with ALA 54 (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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44A LEU* 4.2 5.4 - - + -
45A ILE 3.1 13.2 - - - +
46A ALA* 4.0 12.8 - - + -
24K LEU* 2.9 52.4 + - + -
48K PHE* 3.9 1.5 - - - -
52K THR* 3.5 4.1 - - - +
53K SER* 1.3 80.5 + - - +
55K ILE* 1.3 68.8 + - - +
101K TRP* 4.1 15.3 - - + -
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Residues in contact with ILE 55 (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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44A LEU* 3.5 4.2 - - - -
45A ILE* 2.8 49.1 + - + +
101J TRP* 4.0 19.1 - - + -
10K VAL* 4.1 22.9 - - + -
21K VAL* 3.9 26.5 - - + -
22K ILE 3.2 7.2 - - - +
24K LEU* 4.5 0.4 - - - -
46K ALA* 4.4 6.1 - - + +
47K GLN 4.3 8.3 - - - +
48K PHE* 3.7 28.0 - - + -
52K THR* 3.9 10.5 - - + -
54K ALA* 1.3 82.2 - - - +
56K LYS* 1.3 64.5 + - - +
57K VAL* 4.6 2.7 - - + -
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Residues in contact with LYS 56 (chain K).
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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36A GLU* 3.5 20.3 + - - +
37A LYS 3.4 22.4 + - - -
38A LEU* 4.1 15.9 - - + +
42A GLU* 3.4 24.6 + - + -
43A VAL 3.2 11.9 - - - +
44A LEU* 4.1 10.5 - - + -
20K ASN 3.5 1.4 - - - +
21K VAL* 3.5 2.4 - - - -
22K ILE* 2.7 49.5 + - + +
24K LEU* 4.1 5.8 - - + +
32K PHE* 4.1 7.6 - - + -
55K ILE* 1.3 75.5 - - - +
57K VAL* 1.3 71.7 + - - +
58K ARG* 3.3 33.9 - - - +
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Residues in contact with VAL 57 (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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42A GLU* 3.7 8.7 - - - +
43A VAL* 2.9 30.8 + - + +
45A ILE* 4.4 15.3 - - + -
12K ILE* 4.2 21.8 - - + -
19K VAL* 3.9 22.0 - - + -
20K ASN 3.3 4.0 - - - +
21K VAL* 4.8 3.6 - - + -
55K ILE* 4.6 5.6 - - + -
56K LYS* 1.3 79.2 - - - +
58K ARG* 1.3 63.1 + - - +
59K GLY 4.4 0.2 - - - -
61K ALA* 4.1 8.7 - - + -
63K ILE* 3.8 24.2 - - + -
72K SER* 3.6 22.5 - - - +
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Residues in contact with ARG 58 (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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42A GLU* 3.0 39.2 + - + +
18K GLY 4.4 1.4 - - - +
19K VAL* 3.4 6.7 - - - +
20K ASN* 2.9 44.7 + - + +
22K ILE* 3.9 17.9 - - + +
32K PHE* 3.9 19.8 - - - -
56K LYS* 3.3 31.5 - - + +
57K VAL* 1.3 70.5 - - - +
59K GLY* 1.3 61.5 - - - +
72K SER* 5.6 0.2 - - - -
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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