Contacts of the strand formed by residues 108 - 115 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21I ILE* 4.2 20.6 - - - -
22I PRO 5.4 1.3 + - - -
24I LEU* 6.2 1.3 - - - -
70L LYS* 5.5 1.3 - - - -
44M VAL* 5.6 2.9 - - - -
103M ALA* 3.5 0.6 - - - -
104M THR 2.9 35.9 + - - -
105M PRO 3.9 4.1 + - - -
106M ASP 3.5 2.8 - - - -
107M LYS* 1.3 80.7 - - - +
109M VAL* 1.3 60.9 + - - -
110M TYR* 3.4 9.4 - - - -
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Residues in contact with VAL 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ALA 4.7 8.3 + - - +
18I ALA* 4.6 18.0 - - - +
21I ILE* 4.9 8.8 - - + +
37M THR* 4.3 24.4 - - + +
40M LEU* 3.8 39.7 - - + +
41M ASN* 4.0 10.3 - - + +
44M VAL* 3.9 27.1 - - + -
101M PHE* 4.8 5.2 - - + -
102M ALA 3.6 12.6 - - - +
103M ALA* 4.1 2.9 - - + -
107M LYS 4.0 1.5 + - - +
108M GLY* 1.3 70.5 - - - -
110M TYR* 1.3 62.3 - - - +
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Residues in contact with TYR 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101M PHE* 3.4 9.6 - - - +
102M ALA* 2.8 53.1 + - + +
104M THR* 4.2 9.4 - - + +
107M LYS* 3.5 51.6 + - + +
108M GLY 3.4 14.4 - - - -
109M VAL* 1.3 75.0 - - - +
111M LYS* 1.3 69.4 + - - +
112M THR* 5.2 0.4 - - - -
124M CYS* 3.7 7.6 - - - +
125M PRO* 2.7 50.2 + - + +
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Residues in contact with LYS 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ARG* 5.2 2.6 - - - +
98M THR* 5.7 0.9 - - - +
99M VAL* 4.0 23.1 - - + +
100M TRP 3.7 4.7 - - - +
101M PHE* 3.7 28.9 - - + -
110M TYR* 1.3 85.1 - - - +
112M THR* 1.3 61.2 + - - +
113M ASN* 5.1 1.4 - - - +
52P ILE* 3.7 28.6 + - - +
53P ASP* 3.9 24.2 + - - +
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Residues in contact with THR 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M ILE* 6.0 2.0 - - + -
99M VAL* 3.4 23.4 - - - +
100M TRP* 3.0 40.3 + - + +
101M PHE* 4.8 1.3 - - - +
102M ALA* 5.3 4.9 - - + +
110M TYR* 4.2 2.2 + - - -
111M LYS* 1.3 75.7 - - - +
113M ASN* 1.3 74.7 + - - +
114M THR* 3.8 20.5 + - - +
121M PRO* 4.2 8.9 - - + +
125M PRO* 3.6 33.3 - - + +
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Residues in contact with ASN 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M VAL* 4.2 6.4 - - - +
111M LYS 5.1 1.2 - - - +
112M THR* 1.3 84.4 + - - +
114M THR* 1.3 62.0 + - - +
115M ALA* 3.5 2.6 + - - +
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Residues in contact with THR 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M VAL* 3.3 7.7 - - - +
100M TRP* 3.2 29.7 + - + +
112M THR* 3.3 9.1 + - - +
113M ASN* 1.3 76.9 - - - +
115M ALA* 1.3 66.4 + - - +
118M SER* 4.2 9.0 - - - -
119M SER 3.5 24.9 - - - +
121M PRO* 3.8 25.0 - - + +
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Residues in contact with ALA 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98M THR 4.0 11.7 - - - +
99M VAL* 4.2 3.6 - - + -
100M TRP* 2.9 16.3 + - - -
113M ASN 3.5 3.4 + - - +
114M THR* 1.3 75.4 - - - +
116M VAL* 1.3 63.1 - - - +
117M THR* 3.3 17.0 - - - +
118M SER* 3.2 25.4 + - - +
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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