Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 4PAR
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 ILE 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.5 3.1 - - - -
64A PHE* 2.9 50.8 + - + +
67A LEU* 3.4 30.1 - - + +
68A GLY* 1.3 78.3 - - - +
70A HIS* 1.3 77.0 + - - +
71A ILE* 4.8 4.0 - - + -
119A LYS* 3.7 8.7 - - + +
121A PHE* 3.8 30.5 - - + -
149A GLU 4.5 1.8 - - - +
150A ILE* 4.4 16.4 - - + -
153A ALA* 4.1 26.0 - - + -
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Residues in contact with HIS 70 (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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48A GLN* 4.5 0.7 - - + -
50A VAL* 3.9 20.4 - - + -
60A THR* 2.7 36.5 + - + +
62A LEU 3.4 4.3 - - - +
63A TYR* 3.2 40.6 - + - +
69A ILE* 1.3 82.3 - - - +
71A ILE* 1.3 69.7 + - - +
72A GLU 4.3 0.2 - - - -
113A ILE* 4.7 0.7 - - + -
115A ILE* 3.7 8.0 - - + +
118A HIS* 3.4 33.7 + - + -
119A LYS 2.9 10.4 + - - -
120A ILE* 3.8 21.3 - - + -
121A PHE* 2.9 23.9 + - - +
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Residues in contact with ILE 71 (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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29A VAL* 4.8 4.9 - - + -
30A VAL* 5.8 2.2 - - + -
33A ILE* 3.7 22.4 - - + -
60A THR* 4.2 0.7 - - - -
61A ASP* 3.3 9.4 + - + +
62A LEU* 2.9 63.7 + - + +
64A PHE* 3.8 19.1 - - + -
69A ILE* 4.8 4.0 - - + -
70A HIS* 1.3 80.2 - - - +
72A GLU* 1.3 64.1 + - - +
73A VAL* 4.3 1.1 - - + +
121A PHE* 3.3 9.9 - - + +
123A VAL* 4.3 10.3 - - + -
146A ILE* 3.7 39.5 - - + -
150A ILE* 4.2 3.4 - - + -
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Residues in contact with GLU 72 (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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23A LYS* 3.9 9.2 - - - +
59A LEU 4.7 3.5 - - - +
60A THR* 5.1 7.4 - - + -
61A ASP* 3.8 4.5 - - - +
71A ILE* 1.3 76.5 - - - +
73A VAL* 1.3 75.6 + - - +
74A ASP 3.6 0.7 + - - -
95A PRO* 3.3 14.1 - - + +
96A LEU* 2.6 35.5 + - - +
97A TYR* 3.0 23.8 + - - +
120A ILE* 4.4 9.4 - - + +
121A PHE 2.9 10.1 + - - +
122A ARG* 3.1 32.8 + - + +
123A VAL* 2.9 24.6 + - - +
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Residues in contact with VAL 73 (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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23A LYS* 3.2 11.0 + - + +
25A TYR* 4.1 11.4 - - + +
26A GLU* 4.1 10.3 - - - +
29A VAL* 3.6 39.3 - - + -
30A VAL* 5.3 0.9 - - + -
61A ASP* 2.9 22.9 + - + +
71A ILE* 4.3 1.3 - - + -
72A GLU* 1.3 73.5 - - - +
74A ASP* 1.3 60.0 - - - +
75A GLU* 3.8 29.4 - - + +
97A TYR* 3.1 22.7 + - - -
123A VAL* 3.8 4.5 - - + +
125A VAL* 3.9 19.1 - - + -
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Residues in contact with ASP 74 (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 GLU* 3.6 2.7 + - - +
73A VAL* 1.3 71.0 - - - +
75A GLU* 1.3 74.1 + - - +
76A GLY 3.2 1.0 + - - -
87A TYR* 2.8 28.4 + - - -
96A LEU* 3.5 20.3 - - + +
97A TYR* 3.3 5.2 + - + -
122A ARG* 5.0 8.0 - - + -
123A VAL 2.8 16.1 + - - +
124A ASN* 3.6 24.3 + - - +
125A VAL* 3.3 29.0 + - - +
126A PHE 4.8 0.9 + - - -
129A GLN* 5.5 0.2 + - - -
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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