Contacts of the strand formed by residues 108 - 116 (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 ARG 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PRO* 3.4 6.3 - - - +
97C VAL* 3.3 43.6 + - + +
98C GLN* 5.8 1.3 - - - +
106C ARG* 5.5 9.4 - - + +
107C THR* 1.4 78.0 + - - +
109C PHE* 1.4 68.7 + - - +
128C CYS* 2.8 55.2 + - + -
129C SER* 3.4 21.0 - - - +
130C LYS* 4.3 20.1 - - + +
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Residues in contact with PHE 109 (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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94C ILE* 4.5 13.2 - - + +
96C PRO* 3.9 24.0 - - + -
107C THR* 5.5 6.3 - - + -
108C ARG* 1.4 81.3 - - - +
110C LYS* 1.3 61.3 + - - +
128C CYS* 3.1 2.0 - - - -
129C SER 2.7 41.2 + - - +
130C LYS 4.4 8.9 + - - -
131C GLU* 4.3 2.5 - - - -
132C VAL* 2.9 52.0 - - + -
135C ALA* 3.8 7.5 - - + +
116D ARG* 5.7 2.0 - - - -
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Residues in contact with LYS 110 (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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93C LYS 3.2 1.7 - - - +
94C ILE* 3.0 29.6 + - - -
95C MET* 3.4 33.8 + - + +
97C VAL* 5.1 12.1 - - + -
108C ARG 4.0 0.6 + - - +
109C PHE* 1.3 74.3 - - - +
111C ALA* 1.3 60.6 + - - +
112C PHE* 2.6 42.9 - - + -
126C MET* 4.2 20.9 - - - -
127C LYS 3.0 18.4 - - - +
128C CYS* 3.8 13.7 - - + +
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Residues in contact with ALA 111 (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* 4.7 1.6 - - + -
93C LYS 3.1 6.7 - - - +
94C ILE* 4.2 8.5 - - + -
109C PHE 4.1 0.6 + - - -
110C LYS* 1.3 73.5 - - - +
112C PHE* 1.3 64.6 + - - +
113C VAL* 4.0 3.4 - - + -
125C GLY 3.7 1.6 - - - +
126C MET* 3.3 3.8 - - - -
127C LYS 2.6 34.7 + - - -
135C ALA* 3.9 31.2 - - + +
136C ILE* 4.1 17.7 - - + -
139C ALA* 4.0 4.6 - - + +
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Residues in contact with PHE 112 (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* 3.6 3.8 - - - +
92C LEU* 2.7 52.0 + - + -
93C LYS* 2.9 30.2 + - + +
95C MET* 4.2 15.9 - - + -
110C LYS* 2.6 57.4 - - + -
111C ALA* 1.3 75.1 - - - +
113C VAL* 1.3 57.0 + - - +
124C LEU* 5.5 8.1 - - + -
125C GLY 3.5 2.9 - - - +
126C MET* 3.5 24.0 - - + -
218C LEU* 4.0 19.5 - - + -
219C GLY* 3.9 21.8 - - - -
222C ALA* 6.4 1.6 - - + -
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Residues in contact with VAL 113 (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 8.7 - - + -
90C LYS 3.8 8.3 - - - +
91C VAL* 3.9 22.7 - - + -
92C LEU* 5.0 0.4 - - - -
111C ALA* 4.6 1.8 - - + -
112C PHE* 1.3 79.8 - - - +
114C ALA* 1.3 74.7 + - - +
115C ILE* 4.5 1.8 - - + -
124C LEU* 3.4 7.0 - - - +
125C GLY 2.6 42.1 + - - +
136C ILE* 4.2 10.1 - - + +
139C ALA* 3.1 33.7 - - + -
140C ILE* 4.0 23.6 - - + -
143C ALA* 3.9 2.0 - - + +
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Residues in contact with ALA 114 (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 4.2 0.2 - - - +
89C ASP* 3.3 3.6 - - - -
90C LYS* 2.9 38.5 + - + +
92C LEU* 4.2 21.2 - - + +
113C VAL* 1.3 77.0 - - - +
115C ILE* 1.3 63.0 + - - +
123C GLY 3.4 11.7 - - - +
124C LEU* 4.2 5.4 - - + -
143C ALA* 4.7 0.2 - - - -
197C LYS 6.1 0.7 - - - -
198C LEU* 5.0 17.5 - - + -
201C MET* 5.6 6.9 - - + +
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Residues in contact with ILE 115 (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* 2.9 34.1 - - + -
88C LYS 3.8 4.7 - - - -
89C ASP* 3.3 24.5 - - + +
113C VAL* 4.5 0.4 - - + -
114C ALA* 1.3 73.2 - - - +
116C GLY* 1.4 57.5 + - - +
122C VAL* 3.1 6.4 - - - +
123C GLY 2.8 29.7 + - - +
140C ILE* 3.2 32.8 - - + +
143C ALA* 3.5 13.0 - - + -
144C LYS* 3.1 37.2 - - + -
147C ILE* 4.1 20.4 - - + -
201C MET* 4.5 5.1 - - - +
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Residues in contact with GLY 116 (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* 3.1 20.1 - - - +
88C LYS* 3.3 17.9 + - - +
115C ILE* 1.4 79.7 - - - +
117C ASP* 1.4 73.0 + - - +
121C HIS 3.1 16.2 - - - -
122C VAL* 3.9 5.8 - - - -
201C MET* 3.8 6.2 - - - +
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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