Contacts of the strand formed by residues 111 - 119 (chain C) in PDB entry 6XAV
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 PHE 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 6.1 3.6 - - + -
36C PHE* 3.5 36.8 - + - -
39C LEU* 4.1 32.5 - - + -
40C LYS* 6.0 1.6 - - + -
49C ILE* 5.0 2.5 - - + -
77C ASP* 4.0 31.9 - - + -
78C ASP 3.6 4.2 + - - -
79C ILE* 3.4 20.0 - - + +
80C TYR* 2.5 35.3 + - - +
101C ILE* 4.3 20.0 - - + -
102C ARG 3.5 17.9 - - - +
103C PRO* 3.6 15.0 - - + -
104C PRO* 3.7 11.0 - - + -
110C TYR* 1.3 75.8 - - - +
112C ALA* 1.3 58.5 + - - +
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Residues in contact with ALA 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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79C ILE* 4.5 1.1 - - - -
80C TYR* 4.0 11.9 - - + -
101C ILE* 3.3 5.6 - - - +
102C ARG* 2.7 63.7 + - + +
103C PRO 5.0 2.6 - - - +
104C PRO* 6.2 0.4 - - + -
108C GLU* 6.6 0.4 - - + -
110C TYR 3.6 3.8 + - - +
111C PHE* 1.3 73.6 - - - +
113C LEU* 1.3 60.5 + - - +
114C LEU 3.4 0.2 + - - -
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Residues in contact with LEU 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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65C LEU* 5.0 8.3 - - + -
79C ILE* 4.7 4.9 - - + -
80C TYR 3.7 13.0 + - - +
81C VAL* 5.3 9.0 - - + -
85C GLN* 2.3 59.2 + - + +
89C PHE* 6.3 1.3 - - + -
91C LEU* 5.4 4.5 - - + -
97C ILE* 3.7 33.4 - - + -
99C GLY* 4.7 5.6 - - - +
100C LYS 3.6 17.5 - - - +
101C ILE* 4.1 13.7 - - + -
102C ARG* 5.3 0.4 - - - -
112C ALA* 1.3 71.9 - - - +
114C LEU* 1.3 59.4 + - - +
115C LYS 3.9 16.4 - - - +
116C VAL* 4.5 9.9 - - + +
1019I ASP* 4.7 3.5 - - - +
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Residues in contact with LEU 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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85C GLN* 4.3 4.4 + - - -
100C LYS* 3.1 32.0 + - + +
101C ILE 5.6 0.7 - - - +
102C ARG* 3.6 39.0 - - + +
112C ALA 3.4 4.4 + - - -
113C LEU* 1.3 75.3 - - - +
115C LYS* 1.3 82.3 + - + +
1016I GLU* 3.4 33.7 - - - +
1019I ASP* 3.6 23.3 - - - +
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Residues in contact with LYS 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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99C GLY* 3.4 2.9 - - - -
100C LYS* 3.0 52.0 + - + +
113C LEU* 3.6 6.2 - - - +
114C LEU* 1.3 103.0 - - + +
116C VAL* 1.3 61.3 + - - +
117C ASN* 4.0 11.5 - - - +
1012I GLU* 4.8 17.2 + - - -
1015I ALA* 6.3 2.2 - - + -
1016I GLU* 3.8 21.5 - - + +
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Residues in contact with VAL 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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89C PHE* 3.7 43.5 - - + -
97C ILE* 3.8 30.1 - - + -
98C SER 3.9 6.5 - - - +
99C GLY* 4.3 1.1 - - - -
113C LEU* 4.5 9.5 - - + +
115C LYS* 1.3 72.8 - - - +
117C ASN* 1.3 66.0 + - - +
118C GLU 4.1 1.8 - - - +
119C VAL* 3.7 30.5 - - + -
124C PRO* 4.7 9.0 - - + +
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Residues in contact with ASN 117 (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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50C PHE* 4.7 7.1 - - - -
98C SER 2.7 13.2 + - - +
99C GLY* 3.4 20.0 - - - -
100C LYS* 3.6 23.3 - - - +
115C LYS* 4.0 15.0 - - - +
116C VAL* 1.3 79.5 - - - +
118C GLU* 1.3 60.0 + - + +
123C LYS* 5.4 0.2 - - - -
124C PRO* 3.5 21.6 - - - +
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Residues in contact with GLU 118 (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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96C THR 3.7 2.3 - - - +
97C ILE* 3.9 0.7 - - - -
98C SER* 2.8 50.1 + - - +
116C VAL* 4.1 0.9 - - - +
117C ASN* 1.3 78.4 - - + +
119C VAL* 1.3 61.7 + - - +
120C ASN 4.1 0.4 + - - -
121C PHE* 3.2 36.1 + - - +
122C ASP* 3.3 25.7 + - - +
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Residues in contact with VAL 119 (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 PHE* 6.3 2.0 - - + -
91C LEU* 5.3 5.6 - - + -
95C ASP* 4.9 6.3 - - + -
96C THR 3.3 8.5 - - - +
97C ILE* 4.1 13.0 - - + -
116C VAL* 3.7 22.9 - - + -
118C GLU* 1.3 74.6 - - - +
120C ASN* 1.3 82.9 + - - +
121C PHE 3.2 0.7 - - - -
122C ASP* 3.0 25.4 + - - +
124C PRO* 4.0 23.3 - - + -
127C ALA* 3.7 27.1 - - + +
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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