Contacts of the strand formed by residues 55 - 61 (chain H) in PDB entry 5IYB
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 LYS 55 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H ILE* 4.4 13.2 - - + +
10H PHE 3.1 12.8 - - - +
11H ASP* 2.4 39.8 + - + -
33H GLU* 5.4 9.2 - - + +
53H GLY 3.8 11.4 + - - +
54H ASP* 1.3 80.8 + - - +
56H PHE* 1.3 60.6 + - - +
148H LEU* 2.9 25.4 - - - -
149H ALA* 2.9 19.7 + - + +
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Residues in contact with PHE 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ILE* 3.8 3.1 - - - -
10H PHE* 3.0 50.5 + + + -
12H VAL* 3.9 20.2 - - + -
28H LEU* 4.4 9.6 - - + -
30H CYS* 3.7 32.5 - - - -
39H LEU* 4.9 4.5 - - + -
41H LEU* 5.4 2.2 - - + -
48H TYR* 4.7 5.2 - + + +
50H VAL* 5.8 3.4 - - + -
54H ASP* 4.5 3.6 - - + +
55H LYS* 1.3 74.2 - - - +
57H ARG* 1.3 60.6 + - - +
58H LEU* 3.8 29.3 + - + -
145H MET* 3.5 35.9 - - + -
146H LYS 4.4 2.7 - - - +
148H LEU* 3.8 20.0 - - + +
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Residues in contact with ARG 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H GLU* 2.5 36.6 + - + +
8H ASP 4.0 5.8 - - - +
9H ILE* 4.3 28.7 - - + +
55H LYS 4.2 0.4 + - - -
56H PHE* 1.3 73.4 - - - +
58H LEU* 1.3 60.9 + - - +
59H VAL* 4.5 12.4 - - + +
88H PHE* 5.2 4.0 - - - -
144H LEU 3.8 0.5 - - - +
145H MET* 3.5 4.2 - - - +
146H LYS* 2.9 71.3 + - + +
147H LYS* 4.5 23.0 - - + +
149H ALA 5.2 0.2 - - - +
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Residues in contact with LEU 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H PHE* 4.5 5.2 - - + -
7H GLU* 3.8 0.9 - - - +
8H ASP 3.0 36.8 + - - +
10H PHE* 4.3 14.1 - - + -
39H LEU* 4.1 19.1 - - + -
41H LEU* 4.3 13.9 - - + -
56H PHE* 3.8 29.8 + - + -
57H ARG* 1.3 73.6 - - - +
59H VAL* 1.3 71.8 + - - +
60H ILE* 3.6 32.1 - - + -
123H MET* 4.3 12.1 - - + -
143H LEU* 4.7 5.4 - - + -
144H LEU 3.4 9.9 - - - +
145H MET* 4.4 7.6 - - + -
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET* 6.1 1.3 - - + -
4H ILE* 4.0 24.0 - - + -
6H PHE 3.4 13.9 - - - +
7H GLU* 4.1 24.0 - - + +
57H ARG* 4.5 11.0 - - + +
58H LEU* 1.3 81.8 - - - +
60H ILE* 1.3 72.6 + - - +
61H ALA* 5.3 1.3 - - + -
88H PHE* 3.8 35.0 - - + -
144H LEU* 3.0 40.6 + - + +
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Residues in contact with ILE 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ILE* 4.0 1.2 - - - +
5H LEU* 2.9 38.8 + - + +
6H PHE* 3.0 38.7 + - + +
58H LEU* 3.6 21.5 - - + -
59H VAL* 1.3 83.0 - - - +
61H ALA* 1.3 64.3 + - - +
116H VAL* 6.3 1.6 - - + -
118H TYR* 5.1 1.3 - - - +
123H MET* 4.2 20.0 - - + -
125H LEU* 4.6 12.6 - - + -
141H VAL* 3.5 23.3 - - + -
142H TYR 3.4 13.5 - - - +
143H LEU* 5.1 3.6 - - + -
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Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H MET* 3.7 17.5 - - + -
3H GLY 3.9 9.6 - - - +
4H ILE* 4.5 4.7 - - + -
5H LEU* 4.0 6.3 - - - +
59H VAL* 5.3 1.6 - - + -
60H ILE* 1.3 78.3 - - - +
62H SER* 1.3 60.8 + - - +
63H THR 3.1 23.5 + - - +
64H LEU* 5.6 0.4 - - + -
140H ARG 3.5 2.9 - - - +
141H VAL* 3.9 2.1 - - - -
142H TYR* 3.2 30.9 + - + -
144H LEU* 4.3 11.6 - - + +
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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