Contacts of the strand formed by residues 51 - 57 (chain K) in PDB entry 4DHJ
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 51 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38K VAL* 3.9 21.7 - - + +
39K ILE 3.7 4.5 - - - -
40K ALA* 4.7 10.8 - - + -
49K GLY 5.1 3.6 - - - +
50K GLY* 1.3 78.4 - - - +
52K PHE* 1.3 65.7 + - - +
53K LYS* 4.1 1.8 + - - +
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Residues in contact with PHE 52 (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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38K VAL* 3.4 4.7 - - - +
39K ILE* 2.8 48.9 + - + +
41K GLY* 4.2 5.6 - - - -
47K PHE* 3.9 44.4 - + + -
50K GLY* 3.8 22.9 - - - -
51K THR* 1.3 79.5 - - - +
53K LYS* 1.3 60.8 + - - +
54K LEU* 3.4 17.9 - - + +
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Residues in contact with LYS 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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37K VAL 3.2 8.1 - - - +
38K VAL* 4.6 9.6 - - + +
51K THR 4.1 1.8 + - - -
52K PHE* 1.3 71.8 - - - +
54K LEU* 1.3 65.8 + - - +
55K GLU* 5.6 3.4 - - - +
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Residues in contact with LEU 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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37K VAL* 2.7 47.7 + - + +
39K ILE* 3.9 31.4 - - + -
52K PHE* 3.4 25.8 - - + +
53K LYS* 1.3 79.6 - - - +
55K GLU* 1.3 74.9 + - - +
56K LEU* 6.1 0.9 - - + -
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Residues in contact with GLU 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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34K TYR* 2.7 37.8 + - + +
35K PHE 3.6 1.1 - - - -
36K HIS* 2.8 35.9 + - - +
37K VAL 4.6 0.2 + - - -
53K LYS* 5.6 4.0 - - + +
54K LEU* 1.3 92.7 - - - +
56K LEU* 1.3 60.0 + - - +
68K LYS 3.8 0.5 - - - +
69K VAL* 3.4 21.1 - - - -
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Residues in contact with LEU 56 (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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34K TYR* 3.5 6.9 - - - -
35K PHE* 2.8 59.8 + - + +
37K VAL* 4.6 13.9 - - + -
54K LEU* 4.2 1.3 + - + -
55K GLU* 1.3 74.9 - - - +
57K PHE* 1.3 65.1 + - - +
58K LEU* 3.6 29.2 - - + -
67K PRO* 3.9 22.4 - - + -
68K LYS 3.2 6.3 - - - +
69K VAL* 4.9 3.8 - - - -
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Residues in contact with PHE 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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31K ASN* 4.4 14.6 - - - -
33K ARG* 3.4 39.3 - - + -
34K TYR* 4.4 15.0 - + + -
55K GLU 4.3 0.2 - - - -
56K LEU* 1.3 77.0 - - - +
58K LEU* 1.3 74.9 + - - +
59K PRO* 3.2 20.0 - - + +
60K GLU 5.1 0.7 - - - -
67K PRO* 3.4 2.4 - - - +
68K LYS* 2.7 56.7 + - + +
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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