Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 4Y22
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 4.0 22.0 - - + +
98A VAL 3.5 5.8 - - - +
99A LYS* 3.5 37.5 - - + +
103A GLY 3.6 6.7 + - - +
104A TYR* 1.3 85.7 - - - +
106A PHE* 1.3 62.2 + - - +
107A LYS* 5.5 7.1 - - - +
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Residues in contact with PHE 106 (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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45A PHE* 3.5 28.0 - + - -
58A ILE* 4.5 4.3 - - + -
60A CYS* 3.6 24.0 - - - -
74A GLU* 3.2 39.9 - - + +
96A LEU 3.8 0.3 - - - +
97A THR* 3.9 2.3 - - - +
98A VAL* 3.0 65.5 + - + -
100A LEU* 3.9 11.4 - - + -
104A TYR* 3.5 22.4 - + + +
105A GLU* 1.3 75.3 - - - +
107A LYS* 1.3 74.9 + - - +
108A PHE* 4.7 8.3 - + + -
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Residues in contact with LYS 107 (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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72A GLN* 5.1 2.6 - - - +
74A GLU* 5.2 0.9 - - - +
92A ASP* 5.1 7.3 + - - -
95A ASN* 3.9 35.5 - - + +
96A LEU 3.3 7.4 - - - +
97A THR* 4.0 23.3 + - + +
105A GLU* 5.5 6.3 - - - +
106A PHE* 1.3 86.3 - - - +
108A PHE* 1.3 63.0 + - - +
109A PRO* 4.5 2.6 - - - +
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Residues in contact with PHE 108 (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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42A CYS 3.8 17.0 - - - -
43A LEU* 3.9 15.3 - - + -
60A CYS* 3.7 33.2 - - + -
61A ASN* 3.5 25.6 - - - -
62A SER* 4.3 2.7 - - - -
72A GLN* 4.0 22.7 - - + -
95A ASN* 3.4 3.5 - - - -
96A LEU* 2.5 49.7 + - + +
98A VAL* 5.5 1.1 - - + -
106A PHE* 4.7 9.4 - + + -
107A LYS* 1.3 76.2 - - - +
109A PRO* 1.3 97.8 - - + +
111A ARG* 3.4 31.6 - - - -
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Residues in contact with PRO 109 (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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42A CYS 4.5 0.5 - - - +
72A GLN* 4.1 22.9 - - - +
94A ALA 3.7 9.0 - - - +
95A ASN* 4.0 7.3 - - - +
96A LEU* 4.5 0.7 - - - +
107A LYS 4.5 1.8 - - - +
108A PHE* 1.3 113.3 - - + +
110A ASN* 1.3 60.6 + - - +
111A ARG* 3.3 35.1 + - + +
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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