Contacts of the strand formed by residues 108 - 115 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C ALA 6.2 0.2 - - - -
21C ILE* 4.2 21.5 - - - -
22C PRO 5.4 1.3 + - - -
24C LEU* 6.2 1.1 - - - -
70F LYS* 5.5 1.1 - - - -
44G VAL* 5.6 3.6 - - - -
103G ALA* 3.5 0.3 - - - -
104G THR 2.9 36.1 + - - -
105G PRO 3.9 4.1 + - - -
106G ASP 3.5 2.6 + - - -
107G LYS* 1.3 81.3 - - - +
109G VAL* 1.3 60.9 + - - -
110G TYR* 3.4 9.7 - - - -
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Residues in contact with VAL 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ALA 4.7 8.5 + - - +
18C ALA* 4.6 18.2 - - - +
21C ILE* 4.9 8.3 - - + +
37G THR* 4.3 24.6 - - + +
40G LEU* 3.8 38.8 - - + +
41G ASN* 4.0 11.0 - - + +
44G VAL* 3.9 26.9 - - + -
101G PHE* 4.8 4.3 - - + -
102G ALA 3.6 12.6 - - - +
103G ALA* 4.1 2.9 - - + -
107G LYS 4.8 0.9 - - - +
108G GLY* 1.3 71.6 - - - -
110G TYR* 1.3 64.0 + - - +
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Residues in contact with TYR 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA* 6.6 0.2 - - + -
101G PHE* 3.4 9.5 - - - +
102G ALA* 2.8 52.5 + - + +
104G THR* 4.2 8.6 - - + +
107G LYS* 3.5 52.9 - - + +
108G GLY 3.4 15.3 - - - -
109G VAL* 1.3 74.2 - - - +
111G LYS* 1.3 69.4 + - - +
112G THR* 5.3 0.2 - - - -
124G CYS* 3.7 7.8 - - - +
125G PRO* 2.7 48.8 + - + +
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Residues in contact with LYS 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ARG* 5.2 2.8 - - - +
98G THR* 5.7 0.9 - - - +
99G VAL* 4.0 23.3 - - + -
100G TRP 3.7 4.5 - - - +
101G PHE* 3.7 28.7 - - + -
110G TYR* 1.3 86.3 - - - +
112G THR* 1.3 62.5 + - - +
113G ASN* 5.1 1.2 - - - +
52I ILE* 3.7 28.4 + - - +
53I ASP* 3.9 25.8 + - - +
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Residues in contact with THR 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ILE* 6.0 1.6 - - + -
99G VAL* 3.4 23.2 - - - +
100G TRP* 3.0 41.1 + - + +
101G PHE* 4.8 0.9 - - - +
102G ALA* 5.3 4.7 - - + +
110G TYR* 4.2 3.5 + - - -
111G LYS* 1.3 74.9 - - - +
113G ASN* 1.3 75.0 + - - +
114G THR* 3.8 20.5 + - - +
121G PRO* 4.2 9.5 - - + +
125G PRO* 3.6 33.8 - - + +
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Residues in contact with ASN 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G VAL* 4.2 7.1 - - - +
111G LYS 5.1 1.2 - - - +
112G THR* 1.3 82.8 + - - +
114G THR* 1.3 61.1 + - - +
115G ALA* 3.5 3.1 + - - +
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Residues in contact with THR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G VAL* 3.3 7.5 - - - +
100G TRP* 3.2 29.2 + - + +
112G THR* 3.3 10.0 + - - +
113G ASN* 1.3 76.9 - - - +
115G ALA* 1.3 69.6 + - - +
118G SER* 4.2 8.3 - - - -
119G SER 3.5 24.9 - - - +
121G PRO* 3.8 26.3 - - + +
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Residues in contact with ALA 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G THR 4.0 11.9 - - - +
99G VAL* 4.2 3.6 - - + -
100G TRP* 2.9 16.1 + - - -
113G ASN 3.5 3.1 + - - +
114G THR* 1.3 76.6 - - - +
116G VAL* 1.3 63.4 - - + +
117G THR* 3.3 18.6 - - - +
118G SER* 3.2 23.9 + - - +
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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