Contacts of the strand formed by residues 99 - 109 (chain C) in PDB entry 5IXG
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 99 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B LYS* 4.0 14.1 - - - +
95C PHE* 3.2 4.1 - - - -
96C ASP 2.8 38.6 + - - +
97C GLY 3.3 2.2 + - - -
98C ASP* 1.3 86.7 - - - +
100C PRO* 1.3 80.3 - - + +
101C VAL* 3.5 6.3 - - + +
120C ILE* 6.1 0.2 - - - -
122C SER* 5.6 0.9 - - - +
123C PHE* 3.3 47.9 + - + +
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Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 5.4 2.0 - - + -
46C ARG* 5.5 1.1 - - - +
93C ILE* 3.9 12.3 - - + -
94C LYS 3.6 7.6 - - - +
95C PHE* 3.5 29.1 - - + -
98C ASP 4.0 2.0 - - - +
99C LYS* 1.3 101.5 - - + +
101C VAL* 1.3 62.3 + - - +
102C SER 3.9 0.2 - - - -
120C ILE* 3.8 31.9 - - + +
123C PHE* 3.8 41.0 - - + +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LYS* 6.0 0.4 - - - -
162B LYS* 6.0 7.0 - - + -
94C LYS* 2.8 25.8 + - + +
95C PHE 3.8 4.0 - - - +
96C ASP* 2.9 45.1 - - + +
99C LYS* 3.5 13.5 - - + +
100C PRO* 1.3 74.2 - - - +
102C SER* 1.3 66.0 + - - +
119C LYS* 3.8 9.3 - - + +
120C ILE* 2.9 31.0 + - - +
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Residues in contact with SER 102 (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 ILE* 3.5 7.1 - - - +
94C LYS* 2.9 48.2 + - - +
101C VAL* 1.3 84.2 - - - +
103C VAL* 1.3 65.5 + - - +
104C VAL* 4.1 5.4 - - - +
117C THR* 4.4 5.2 - - - -
118C LEU 3.1 13.7 - - - -
119C LYS* 3.9 22.6 + - - -
120C ILE* 3.8 5.3 - - - +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL* 4.2 9.0 - - + -
89C TYR* 3.1 32.6 + - + +
91C GLY 3.8 16.4 - - - -
92C THR 3.4 12.6 - - - +
93C ILE* 4.2 11.4 - - + -
102C SER* 1.3 77.8 - - - +
104C VAL* 1.3 63.7 + - - +
117C THR* 3.2 4.3 - - - +
118C LEU* 2.7 43.0 + - + +
120C ILE* 4.0 11.4 - - + -
201C OTP 4.0 30.3 - - + -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 3.9 0.4 - - - -
91C GLY* 3.3 0.3 - - - -
92C THR* 2.8 36.3 + - - +
94C LYS* 3.7 40.3 + - + +
102C SER* 4.1 6.5 - - - +
103C VAL* 1.3 74.1 - - - +
105C GLY* 1.3 60.5 + - - +
117C THR* 3.9 23.3 - - + +
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Residues in contact with GLY 105 (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 TYR* 3.4 4.9 + - - -
90C LYS 3.2 14.1 - - - -
91C GLY* 3.7 1.3 - - - -
104C VAL* 1.3 79.0 - - - +
106C ASN* 1.3 73.4 + - - -
115C PRO* 3.4 4.9 - - - +
116C LEU 2.9 33.5 + - - -
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Residues in contact with ASN 106 (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 ASN* 3.8 2.1 - - - +
89C TYR* 3.4 9.2 - - - -
90C LYS* 2.9 34.5 + - + +
105C GLY* 1.3 78.7 + - - -
107C LEU* 1.3 59.3 - - - +
108C THR* 4.0 1.1 + - - -
113C THR* 3.9 22.0 - - + +
114C LYS* 3.3 5.4 - - - +
115C PRO* 3.3 28.6 - - - +
116C LEU 4.1 0.4 - - - +
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Residues in contact with LEU 107 (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 ALA* 4.7 0.4 - - + -
88C ASN 3.4 15.5 - - - +
89C TYR* 4.2 5.8 - - + -
106C ASN* 1.3 72.0 - - - +
108C THR* 1.3 67.8 + - - +
109C LEU* 4.2 23.6 - - + -
113C THR* 3.3 1.9 - - - -
114C LYS 2.9 34.8 + - - +
116C LEU* 4.0 28.4 - - + +
144C PHE* 4.3 17.3 - - + -
149C PHE* 3.4 25.7 - - + -
165C LEU* 5.0 0.4 - - + -
201C OTP 4.1 37.7 - - + -
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Residues in contact with THR 108 (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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86C GLN 5.3 2.9 - - - +
87C ALA* 3.2 9.4 - - - +
88C ASN* 2.8 51.8 + - + +
106C ASN 4.0 1.2 + - - -
107C LEU* 1.3 70.5 - - - +
109C LEU* 1.3 62.6 + - - +
111C GLY* 5.1 6.3 - - - +
112C VAL 3.3 12.1 - - - +
113C THR* 2.6 30.3 + - - +
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Residues in contact with LEU 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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59C ILE* 4.0 17.3 - - + -
79C PHE* 4.1 13.2 - - + -
86C GLN 5.1 0.7 - - - -
87C ALA* 4.0 5.6 - - + +
107C LEU* 4.2 11.7 - - + -
108C THR* 1.3 77.3 - - - +
110C HIS* 1.3 74.3 + - - +
111C GLY 3.3 1.1 - - - -
112C VAL* 2.9 18.4 + - - +
144C PHE* 4.1 24.2 - - + -
149C PHE* 3.5 31.3 - - + -
151C LEU* 3.8 23.3 - - + -
201C OTP 3.9 31.0 - - + -
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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