Contacts of the helix formed by residues 152 - 156 (chain A) in PDB entry 5IVI
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 TYR 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 4.0 24.9 + + - -
149A GLY 4.6 0.8 + - - -
150A PRO 3.2 0.6 - - - -
151A ASP* 1.3 84.2 - - + +
153A PHE* 1.3 67.2 + - - +
154A ILE 3.2 0.2 - - - -
155A LYS* 3.2 28.7 + - - +
156A LYS* 4.4 3.3 - - - +
453A LEU* 4.6 5.2 - - - +
476A THR 3.5 15.7 + - - -
477A TYR 4.3 1.1 - - - -
478A PHE 3.6 25.8 - - - +
479A PHE 3.4 19.8 + - - -
480A TRP* 3.3 42.6 - + + -
484A ALA* 3.7 13.2 - - - +
485A LYS 5.1 1.0 + - - -
497A ILE* 3.7 43.6 - - + +
501A THR* 4.1 10.3 + - + +
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Residues in contact with PHE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.6 24.9 - - + -
150A PRO* 3.1 4.5 + - + +
152A TYR* 1.3 81.2 - - - +
154A ILE* 1.3 56.5 + - - +
155A LYS 3.0 0.2 - - - -
156A LYS* 2.8 32.7 + - - +
158A VAL* 4.3 9.8 - - + +
160A LEU* 3.6 37.5 - - + -
215A PHE* 3.8 29.6 - + - -
478A PHE* 3.5 46.9 + + - -
479A PHE* 4.0 13.5 - + - -
501A THR* 4.2 18.1 - - + +
504A TRP* 4.3 13.7 - - + -
505A THR* 4.4 8.7 - - - -
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 3.9 3.6 - - + -
53A ASP* 3.8 23.4 - - + +
54A SER 3.6 19.5 - - - +
55A TYR* 3.6 42.2 - - + -
117A TYR* 4.2 12.1 - - + +
118A THR* 4.5 8.7 - - - +
119A ASN* 3.0 28.8 + - + +
150A PRO* 3.0 33.8 + - + +
151A ASP 3.6 13.9 - - - +
153A PHE* 1.3 74.4 - - + +
155A LYS* 1.3 55.6 + - - +
156A LYS 3.1 8.5 - - - -
158A VAL* 5.9 2.5 - - - +
160A LEU* 5.6 2.2 - - + -
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Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 4.0 21.8 - - - +
53A ASP* 3.1 33.4 - - - +
119A ASN* 4.4 3.0 + - - -
151A ASP 4.3 7.4 - - - +
152A TYR* 3.2 19.2 + - + +
153A PHE 3.0 0.6 - - - -
154A ILE* 1.3 78.5 - - - +
156A LYS* 1.3 70.2 + - + +
157A ASP* 4.7 2.9 - - - +
494A TYR* 2.4 49.6 + - - +
497A ILE* 5.9 5.0 - - + +
498A GLU* 4.1 15.8 + - - +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN* 3.1 16.3 + - - -
152A TYR 4.4 2.9 - - - +
153A PHE* 2.8 26.3 + - + +
154A ILE* 3.8 2.1 - - - +
155A LYS* 1.3 96.2 + - + +
157A ASP* 1.3 62.3 + - - +
158A VAL* 3.1 15.0 + - + +
498A GLU* 4.3 14.8 + - - +
501A THR* 4.2 15.0 - - - +
502A GLY* 4.2 21.1 - - - +
505A THR* 3.5 37.0 - - + +
518A ILE* 5.2 5.1 - - - +
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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