Contacts of the strand formed by residues 119 - 123 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73F ARG* 3.2 24.4 + - + +
74F GLN* 2.8 29.6 + - - +
75F ILE 3.6 7.1 + - - +
112F ASN* 3.1 2.7 - - - -
117F ASN 3.7 3.1 + - - +
118F CYS* 1.3 75.5 - - - +
120F VAL* 1.3 62.7 + - - +
121F VAL* 3.6 16.5 + - - +
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F LEU* 4.5 8.3 - - + -
75F ILE* 3.1 24.9 - - + +
77F VAL* 3.6 27.6 - - + -
108F ALA* 3.3 23.3 - - + -
111F LEU* 4.6 11.4 - - + -
112F ASN* 2.5 40.3 + - - +
118F CYS* 3.6 24.2 - - - -
119F ASN* 1.3 73.7 - - - +
121F VAL* 1.3 62.8 + - - +
122F PRO* 3.6 7.3 - - - +
105H GLU* 5.7 0.3 - - - +
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ILE 2.8 8.9 + - - +
76F HIS* 3.2 31.1 - - + +
77F VAL 2.8 24.7 + - - -
119F ASN* 3.8 21.3 - - - +
120F VAL* 1.3 76.5 - - - +
122F PRO* 1.3 76.7 - - + +
123F HIS* 3.5 19.1 - - + +
124H PHE* 4.2 35.7 - - + -
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Residues in contact with PRO 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F VAL* 3.5 7.6 - - + +
104F ALA* 3.1 33.7 - - + +
105F GLU* 3.8 13.9 - - + +
108F ALA* 3.6 14.4 - - + -
120F VAL 3.6 9.6 - - - +
121F VAL* 1.3 91.1 - - + +
123F HIS* 1.3 75.8 + - - +
124F PHE 4.1 1.1 - - - +
105H GLU* 4.6 17.7 - - - +
124H PHE* 5.2 4.3 + - - +
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Residues in contact with HIS 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F HIS* 2.9 37.1 + + + -
77F VAL 2.8 15.0 + - - +
78F ILE* 3.6 15.3 - - + -
79F ASP 3.2 18.0 + - - -
104F ALA* 3.9 3.4 - - - +
121F VAL* 3.5 20.6 - - + +
122F PRO* 1.3 87.4 + - - +
124F PHE* 1.3 53.7 + - - +
125F ASN* 2.5 32.1 + - - +
130F PHE* 4.2 5.3 - + + -
134F PHE* 4.1 16.0 - + - -
123H HIS* 5.8 1.3 - - - +
124H PHE* 3.9 13.9 + - + -
125H ASN* 3.3 36.0 + - - -
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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