Contacts of the strand formed by residues 119 - 123 (chain B) in PDB entry 1R4N
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 ASN 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ARG* 3.2 25.3 + - + +
74B GLN* 2.8 29.5 + - - +
75B ILE 3.6 8.5 + - - +
112B ASN* 3.2 2.5 - - - -
117B ASN 3.7 3.8 + - - +
118B CYS* 1.3 75.3 - - - +
120B VAL* 1.3 61.1 + - - +
121B VAL* 3.7 14.6 + - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 4.5 7.9 - - + -
75B ILE* 3.1 23.8 - - + +
77B VAL* 3.6 27.8 - - + -
108B ALA* 3.4 23.3 - - + -
111B LEU* 4.6 12.8 - - + -
112B ASN* 2.5 40.3 + - - +
118B CYS* 3.7 23.6 - - - -
119B ASN* 1.3 71.8 - - - +
121B VAL* 1.3 63.4 + - - +
122B PRO* 3.6 7.6 - - - +
105D GLU* 5.7 0.2 - - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE 2.8 8.7 + - - -
76B HIS* 3.2 32.8 - - + +
77B VAL 2.8 24.0 + - - -
119B ASN* 4.0 20.2 - - - +
120B VAL* 1.3 76.9 - - - +
122B PRO* 1.3 74.1 - - + +
123B HIS* 3.5 18.7 - - + +
124D PHE* 4.2 35.2 - - + -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.5 7.6 - - + +
104B ALA* 3.2 33.0 - - + +
105B GLU* 3.8 14.1 - - + +
108B ALA* 3.6 13.9 - - + -
120B VAL 3.6 9.0 - - - +
121B VAL* 1.3 92.9 - - + +
123B HIS* 1.3 72.7 + - - +
124B PHE 4.1 0.9 - - - +
105D GLU* 4.6 16.8 - - - +
123D HIS* 6.1 0.2 - - - -
124D PHE* 5.3 3.8 + - - +
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Residues in contact with HIS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B HIS* 2.9 37.1 + + + -
77B VAL 2.8 14.7 + - - +
78B ILE* 3.6 16.7 - - + -
79B ASP 3.2 18.4 + - - -
104B ALA* 3.9 3.7 - - - +
121B VAL* 3.5 20.4 - - + +
122B PRO* 1.3 86.0 + - - +
124B PHE* 1.3 53.4 + - - +
125B ASN* 2.5 31.8 + - - +
130B PHE* 4.2 5.7 - + + -
134B PHE* 4.0 17.1 - + - -
123D HIS* 5.8 1.5 + - - +
124D PHE* 3.9 14.2 + - + -
125D ASN* 3.4 35.4 + - - -
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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