Contacts of the strand formed by residues 27 - 31 (chain B) in PDB entry 5HKE
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 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU* 1.3 79.9 - - - +
28B VAL* 1.3 66.4 + - - +
29B ILE* 3.5 8.6 + - + +
54B VAL* 3.4 2.9 - - - -
55B GLY 2.9 36.0 + - - +
56B ILE* 4.6 1.6 - - - -
57B VAL* 3.4 35.5 + - - +
311B THR* 3.5 24.5 + - - +
312B TYR 3.5 14.6 - - - +
313B PRO* 3.8 18.5 - - + +
314B PHE* 3.8 10.8 - - - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 5.3 0.7 - - + -
27B GLU* 1.3 74.4 - - - +
29B ILE* 1.3 63.3 + - - +
30B ILE* 4.2 4.0 - - + -
52B ILE* 4.2 12.6 - - + -
53B GLY 3.4 11.7 - - - +
54B VAL* 4.7 0.4 - - - +
285B LEU* 4.0 12.8 - - + -
287B TYR* 3.6 32.1 - - + +
298B VAL* 3.9 28.3 - - + -
310B VAL 5.5 0.4 - - - +
311B THR* 3.1 8.9 - - - -
312B TYR* 2.9 49.9 + - + +
314B PHE* 3.6 8.0 - - + -
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Residues in contact with ILE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 3.7 14.8 - - + +
28B VAL* 1.3 80.1 - - - +
30B ILE* 1.3 67.4 + - - +
31B THR* 4.2 2.0 - - - +
52B ILE* 3.5 0.2 - - - -
53B GLY 2.9 27.8 + - - -
55B GLY* 3.5 35.2 - - - +
56B ILE* 3.6 16.4 - - - +
57B VAL* 3.8 19.3 - - + -
62B PRO* 3.9 20.9 - - + -
63B LEU 4.6 0.4 - - - +
64B TYR* 2.8 38.2 + - + +
309B LEU* 4.4 8.5 - - + -
310B VAL 3.5 5.6 - - - +
311B THR* 4.4 1.8 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.8 3.8 - - + -
29B ILE* 1.3 74.3 - - - +
31B THR* 1.3 69.6 + - - +
32B PRO* 3.6 9.8 - - + +
51B LEU 3.2 8.3 - - - +
52B ILE* 3.9 32.1 - - + -
298B VAL* 4.4 9.4 - - + -
299B THR 4.1 13.5 - - - +
300B LEU* 3.8 18.2 - - + -
309B LEU* 3.5 7.3 - - - +
310B VAL* 2.8 57.2 + - + +
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Residues in contact with THR 31 (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 ILE* 4.2 0.2 - - - +
30B ILE* 1.3 72.5 - - - +
32B PRO* 1.3 70.0 - - - +
35B TYR* 3.6 36.3 - - + -
37B PHE* 3.6 17.7 - - + -
48B HIS* 4.0 3.6 - - + -
49B LYS 4.4 0.3 - - - +
50B SER* 3.2 3.5 - - - -
51B LEU* 2.8 41.9 + - - -
62B PRO* 3.8 3.8 - - - +
64B TYR* 2.8 30.4 + - - -
309B LEU* 3.5 13.6 - - + +
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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