Contacts of the strand formed by residues 108 - 115 (chain C) in PDB entry 6XXD
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 GLY 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B LYS* 5.6 1.8 - - - -
44C VAL* 5.6 3.1 - - - -
103C ALA* 3.5 0.6 - - - -
104C THR 2.9 36.0 + - - -
105C PRO 3.9 4.3 + - - -
106C ASP 3.5 2.4 - - - -
107C LYS* 1.3 80.7 - - - +
109C VAL* 1.3 61.8 + - - -
110C TYR* 3.4 9.5 - - - -
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Residues in contact with VAL 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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37C THR* 4.3 24.8 - - + +
40C LEU* 3.8 39.3 - - + +
41C ASN* 4.0 10.5 - - + +
44C VAL* 3.9 27.8 - - + -
101C PHE* 4.8 4.5 - - + -
102C ALA 3.6 12.8 - - - +
103C ALA* 4.1 3.1 - - + +
107C LYS 4.8 1.5 - - - +
108C GLY* 1.3 70.2 - - - -
110C TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 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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101C PHE* 3.4 9.7 - - - +
102C ALA* 2.8 52.7 + - + +
104C THR* 4.2 9.8 - - + +
107C LYS* 3.5 54.1 - - + +
108C GLY 3.4 14.8 - - - -
109C VAL* 1.3 73.1 - - - +
111C LYS* 1.3 70.2 + - - +
112C THR* 5.2 0.9 - - - -
124C CYS* 3.7 7.6 - - - +
125C PRO* 2.7 49.5 + - + +
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Residues in contact with LYS 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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30C ARG* 5.2 2.4 - - - +
98C THR* 5.7 0.9 - - - +
99C VAL* 4.0 23.3 - - + -
100C TRP 3.7 3.8 - - - -
101C PHE* 3.7 27.8 - - + -
110C TYR* 1.3 86.8 - - - +
112C THR* 1.3 60.9 + - - +
113C ASN* 5.1 1.6 - - - +
52F ILE* 3.7 28.2 + - - +
53F ASP* 3.9 23.9 + - - +
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Residues in contact with THR 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 ILE* 6.0 1.6 - - + -
99C VAL* 3.4 23.4 - - - +
100C TRP* 3.0 40.5 + - + +
101C PHE* 4.8 0.9 - - - +
102C ALA* 5.3 4.9 - - + +
110C TYR* 4.2 3.1 + - - -
111C LYS* 1.3 74.9 - - - +
113C ASN* 1.3 73.1 + - - +
114C THR* 3.8 21.5 + - - +
121C PRO* 4.2 9.0 - - + +
125C PRO* 3.6 32.5 - - + +
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Residues in contact with ASN 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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99C VAL* 4.2 7.0 - - - +
111C LYS 5.1 1.2 - - - +
112C THR* 1.3 82.3 + - - +
114C THR* 1.3 61.2 + - - +
115C ALA* 3.5 3.1 + - - +
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Residues in contact with THR 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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99C VAL* 3.3 8.1 - - - +
100C TRP* 3.2 29.7 + - + +
112C THR* 3.3 8.6 + - - -
113C ASN* 1.3 76.6 - - - +
115C ALA* 1.3 67.0 + - - +
118C SER* 4.2 9.0 - - - -
119C SER 3.5 25.6 - - - +
121C PRO* 3.8 24.7 - - + +
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Residues in contact with ALA 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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98C THR 4.0 11.4 - - - +
99C VAL* 4.2 3.6 - - + -
100C TRP* 2.9 16.9 + - - -
113C ASN 3.5 3.5 + - - +
114C THR* 1.3 75.5 - - - +
116C VAL* 1.3 63.3 - - + +
117C THR* 3.8 17.9 - - - +
118C SER* 3.2 24.3 + - - +
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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