Contacts of the helix formed by residues 49 - 56 (chain J) in PDB entry 5A15
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 SER 49 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43J LEU 4.5 3.3 + - - -
46J ILE* 2.4 43.4 + - - +
47J PRO 3.0 1.2 - - - -
48J HIS* 1.3 80.7 - - - +
50J LEU* 1.3 58.3 + - - +
51J LEU* 4.0 3.4 + - - +
52J TRP* 3.2 13.0 + - - +
53J LYS* 2.8 29.4 + - - +
89J LEU* 6.0 0.9 - - - +
113J PHE 4.1 3.8 - - - -
114J GLN* 3.9 21.1 - - - -
115J LEU* 4.3 6.3 - - - -
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Residues in contact with LEU 50 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J SER* 1.3 74.6 - - - +
51J LEU* 1.3 59.1 + - - +
53J LYS* 3.1 11.3 + - + +
54J MET* 2.9 51.7 + - + +
112J TYR* 3.3 56.1 - - + +
113J PHE* 3.2 30.6 + - + +
114J GLN* 3.5 19.8 + - - +
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Residues in contact with LEU 51 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J LEU* 5.5 1.1 - - + -
43J LEU* 3.5 26.8 - - + +
49J SER* 3.5 3.7 + - - +
50J LEU* 1.3 80.1 - - - +
52J TRP* 1.3 60.9 + - - +
54J MET* 4.3 13.5 - - - -
55J PHE* 3.2 48.8 + - + +
75J ILE* 4.6 8.7 - - + -
82J PHE* 4.3 18.2 - - + -
85J ILE* 5.0 1.8 - - + -
89J LEU* 3.5 33.4 - - + -
113J PHE* 3.9 37.8 + - + -
115J LEU* 6.2 1.3 - - + -
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Residues in contact with TRP 52 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LEU 3.4 8.8 + - - +
44J ILE* 3.5 33.2 + - + +
46J ILE 3.2 20.4 - - - +
47J PRO* 3.7 21.7 - - + +
48J HIS* 3.2 44.4 - + - -
49J SER* 3.2 9.2 + - - +
50J LEU 3.1 0.6 - - - -
51J LEU* 1.3 77.8 - - - +
53J LYS* 1.3 81.7 + - + +
56J SER* 2.4 63.5 + - - -
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Residues in contact with LYS 53 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J HIS 5.8 0.7 - - - -
49J SER 2.8 17.4 + - - +
50J LEU* 3.1 13.0 + - + +
52J TRP* 1.3 90.7 - - + +
54J MET* 1.3 62.9 + - + +
56J SER* 4.1 10.3 + - - +
114J GLN* 5.9 0.7 - - - +
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Residues in contact with MET 54 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 4.3 8.1 - - - -
50J LEU* 2.9 42.0 + - + +
51J LEU* 3.8 13.9 - - - +
52J TRP 3.2 0.2 - - - -
53J LYS* 1.3 81.1 - - + +
55J PHE* 1.3 75.2 + - + +
56J SER 3.7 3.1 + - - +
65J LEU* 5.8 3.3 - - - +
66J ALA* 6.1 4.5 - - + +
73J PHE* 6.4 1.1 - - + -
74J PHE 4.9 3.8 - - - +
75J ILE* 3.5 33.0 - - + -
112J TYR* 6.0 0.7 - - - -
113J PHE* 6.2 0.4 - - - -
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Residues in contact with PHE 55 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 3.3 39.0 - + - -
27J VAL* 4.0 8.3 - - + -
29J LEU* 3.6 26.0 - - + -
40J HIS* 3.2 30.6 + + + +
43J LEU* 3.7 25.8 - - + -
44J ILE* 4.2 9.9 - - + -
51J LEU* 3.2 43.8 + - + +
52J TRP 3.9 0.9 - - - -
54J MET* 1.3 94.5 - - + +
56J SER* 1.3 60.9 + - - +
57J PRO* 3.6 2.3 - - - +
73J PHE* 3.9 32.5 - + + -
75J ILE* 5.1 0.9 - - + -
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Residues in contact with SER 56 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 5.0 1.1 - - - -
44J ILE* 4.0 5.2 - - - +
52J TRP* 2.4 65.4 + - - -
53J LYS* 4.3 10.0 - - - +
54J MET 3.4 3.6 - - - +
55J PHE* 1.3 77.6 - - - +
57J PRO* 1.4 72.9 - - - +
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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