Contacts of the strand formed by residues 88 - 93 (chain C) in PDB entry 4KZZ
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ALA 4.2 0.8 + - - -
87C LEU* 1.3 76.6 - - - +
89C ASP* 1.3 71.3 + - - +
90C LYS* 4.1 4.9 + - + +
115C ILE* 3.8 1.2 - - - -
116C GLY 3.3 26.9 + - - +
117C ASP* 4.9 0.4 - - - +
118C TYR* 4.8 15.7 + - + +
201C MET* 3.9 30.1 - - + +
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Residues in contact with ASP 89 (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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87C LEU* 4.4 5.9 - - - +
88C LYS* 1.3 88.8 - - - +
90C LYS* 1.3 60.7 + - - +
91C VAL* 4.2 3.3 + - + +
113C VAL* 4.2 9.2 - - + -
114C ALA 3.3 6.3 - - - +
115C ILE* 3.3 23.7 - - + +
140C ILE* 3.5 33.9 - - + +
144C LYS* 3.9 9.4 + - - -
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Residues in contact with LYS 90 (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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88C LYS* 4.1 5.5 + - + +
89C ASP* 1.3 76.2 - - - +
91C VAL* 1.3 80.2 + - - +
92C LEU* 3.5 16.3 + - + +
113C VAL* 4.4 1.1 - - - -
114C ALA* 2.9 34.2 + - + +
197C LYS* 4.2 29.6 - - + +
201C MET* 5.0 15.7 - - + +
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Residues in contact with VAL 91 (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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89C ASP* 4.2 3.1 + - + +
90C LYS* 1.3 91.1 + - - +
92C LEU* 1.3 61.7 + - - +
93C LYS 3.9 10.8 - - - +
94C ILE* 4.1 24.2 - - + -
111C ALA* 4.7 3.6 - - + -
112C PHE 3.6 11.2 - - - +
113C VAL* 3.9 13.0 - - + -
136C ILE* 3.7 36.1 - - + -
140C ILE* 5.8 0.9 - - + -
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Residues in contact with LEU 92 (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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90C LYS* 4.1 20.6 - - + +
91C VAL* 1.3 77.2 - - - +
93C LYS* 1.4 61.7 + - + +
112C PHE* 2.7 25.7 + - + +
114C ALA* 4.2 21.3 - - + -
124C LEU* 4.2 17.0 - - + -
194C VAL* 4.0 37.6 - - + +
197C LYS* 4.6 18.8 - - + +
198C LEU* 5.6 5.8 - - + +
218C LEU* 5.4 1.7 - - + +
222C ALA* 4.6 8.7 - - + -
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Residues in contact with LYS 93 (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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91C VAL* 3.7 3.5 - - - +
92C LEU* 1.4 82.5 - - - +
94C ILE* 1.2 70.0 + - - +
95C MET* 3.0 44.5 - - + +
110C LYS 3.2 0.9 - - - +
111C ALA* 3.1 6.8 - - - -
112C PHE* 2.9 38.0 + - + -
218C LEU* 1.8 55.6 - - + +
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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