Contacts of the strand formed by residues 48 - 52 (chain B) in PDB entry 5KAL
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 ARG 48 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 6.1 0.2 - - - -
40B VAL* 5.3 1.3 - - - -
46B LEU 3.6 17.7 + - - +
47B MET* 1.3 77.5 - - - +
49B LEU* 1.3 61.5 + - - +
50B TYR* 3.9 22.0 - - + -
70B VAL 3.8 0.3 - - - +
71B VAL* 3.3 9.1 - - - +
72B LEU 2.9 36.8 + - - +
73B ASN* 3.7 1.0 - - - +
74B LYS* 3.1 59.0 - - - +
77B VAL* 4.2 23.2 - - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.2 64.0 + - + +
36B VAL* 4.2 8.1 - - + -
37B LEU* 4.1 28.5 - - + +
40B VAL* 4.3 18.2 - - + -
47B MET 4.4 0.4 + - - -
48B ARG* 1.3 74.2 - - - +
50B TYR* 1.3 63.6 + - - +
69B PHE* 3.9 29.4 - - + -
70B VAL 3.6 13.0 - - - +
71B VAL* 4.4 9.9 - - + -
137B ILE* 4.4 3.8 - - + -
220B PRO* 3.3 12.8 - - - +
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ARG* 3.9 27.8 - - + -
49B LEU* 1.3 84.5 - - - +
51B THR* 1.3 62.9 + - - +
69B PHE* 3.3 8.6 - - - -
70B VAL* 2.9 52.4 + - + +
72B LEU* 3.9 17.9 - - + -
77B VAL* 3.8 35.5 - - + +
145B VAL* 4.3 12.1 - - + -
215B VAL* 4.7 5.4 + - + -
218B VAL* 4.1 29.8 + - + -
219B GLU 4.6 1.1 - - - -
220B PRO* 3.7 37.3 - - + +
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Residues in contact with THR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 5.9 0.7 - - + -
33B TYR* 3.7 4.5 - - - -
50B TYR* 1.3 76.6 - - - +
52B PHE* 1.3 75.8 + - - +
55B THR* 5.0 9.6 - - + -
56B VAL* 3.8 19.8 - - + +
67B VAL* 4.1 18.8 - - + -
68B ASP 3.5 9.6 - - - +
69B PHE* 3.7 13.4 - - + -
145B VAL* 4.0 8.0 - - - +
219B GLU 5.2 1.6 - - - +
220B PRO* 2.9 22.5 + - - +
221B LEU* 3.4 26.6 - - + +
222B PRO* 4.7 2.4 - - + +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B THR* 1.3 83.9 - - - +
53B GLY* 1.3 72.9 + - - +
55B THR* 4.9 4.2 + - - -
56B VAL* 3.6 13.9 - - - -
67B VAL* 5.2 0.3 - - - -
68B ASP* 2.9 55.2 + - + +
69B PHE 3.7 28.5 - - - -
70B VAL* 4.0 12.8 - - + -
138B THR* 4.4 10.8 - - + -
144B GLY* 4.1 17.7 - - - -
145B VAL* 3.9 27.1 - - + -
148B SER* 3.6 19.7 - - - +
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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
------------------------------------------------------------
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