Contacts of the strand formed by residues 119 - 124 (chain C) 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 LYS 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU 4.9 3.2 + - - -
68C GLY 3.4 8.0 + - - +
69C ILE* 3.7 35.4 - - + +
70C HIS* 2.9 27.5 + - - +
93C ASP* 4.6 8.1 - - - +
117C GLY 4.4 7.6 - - - +
118C HIS* 1.3 76.8 - - - +
120C ILE* 1.3 61.9 + - - +
121C PHE* 4.2 20.8 - - + -
149C GLU* 5.7 4.0 - - - +
153C ALA* 4.6 9.1 - - - +
156C LYS* 5.8 4.2 - - - +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 4.2 14.8 - - + -
70C HIS* 3.7 21.8 - - + +
72C GLU* 4.5 10.1 - - + +
92C ILE* 5.1 2.1 - - - +
93C ASP* 3.1 43.6 + - - +
94C GLU 3.8 0.2 - - - -
95C PRO* 3.6 31.2 - - + -
115C ILE* 5.8 3.8 - - + -
118C HIS* 4.1 2.2 + - + +
119C LYS* 1.3 76.3 - - - +
121C PHE* 1.3 76.8 + - - +
122C ARG* 3.9 30.9 + - + +
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Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 3.8 27.1 - - + -
70C HIS 2.9 19.0 + - - +
71C ILE* 3.4 7.4 - - + +
72C GLU 2.9 25.6 + - - -
119C LYS* 4.5 22.4 - - + -
120C ILE* 1.3 80.5 - - - +
122C ARG* 1.3 62.8 + - - +
145C LYS* 5.5 4.9 - - - +
146C ILE* 4.1 33.9 - - + -
149C GLU* 3.5 39.5 - - + -
150C ILE* 6.0 0.7 - - + -
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLU* 3.2 28.3 + - - +
74C ASP* 4.8 9.4 - - + -
91C GLN 4.3 1.0 + - - -
92C ILE* 2.8 42.3 + - - +
94C GLU 2.7 32.3 + - - -
95C PRO* 4.2 0.2 - - - +
96C LEU* 3.6 34.7 - - - +
120C ILE* 3.9 19.6 + - + +
121C PHE* 1.3 77.6 - - - +
123C VAL* 1.3 66.1 + - - +
124C ASN* 4.0 15.3 + - - +
142C GLN* 3.7 7.3 - - - +
145C LYS* 4.6 8.0 + - - -
146C ILE* 4.6 4.9 - - - +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.1 30.1 - - + -
71C ILE* 4.4 8.1 - - + -
72C GLU 2.9 10.9 + - - +
73C VAL* 3.6 6.7 - - - -
74C ASP 2.8 23.9 + - - +
122C ARG* 1.3 77.6 - - - +
124C ASN* 1.3 61.9 + - - +
125C VAL* 3.4 19.5 + - + +
139C ILE* 4.5 14.4 - - + +
142C GLN* 3.3 21.8 - - + +
143C ILE* 4.9 3.4 - - + -
146C ILE* 3.6 26.2 - - + -
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Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ASP* 2.8 35.1 - - - +
122C ARG* 4.4 16.1 + - - +
123C VAL* 1.3 71.8 - - - +
125C VAL* 1.3 60.1 + - - +
126C PHE 3.4 8.5 - - - +
134C GLN* 3.0 21.3 - - - +
139C ILE* 4.9 1.0 - - - +
142C GLN* 3.1 25.5 + - - +
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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