Contacts of the strand formed by residues 108 - 115 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D LYS* 5.2 1.3 - - - +
44E VAL* 5.6 3.1 - - - -
103E ALA* 3.5 0.5 - - - -
104E THR 2.9 35.8 + - - -
105E PRO 3.9 4.9 + - - -
106E ASP 3.5 2.2 - - - -
107E LYS* 1.3 81.5 - - - +
109E VAL* 1.3 61.0 + - - -
110E TYR* 3.4 10.2 - - - -
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Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E THR* 4.3 24.0 - - + +
40E LEU* 3.8 38.6 - - + +
41E ASN* 4.0 10.8 - - + +
44E VAL* 3.9 27.6 - - + -
101E PHE* 4.8 4.5 - - + -
102E ALA 3.6 12.1 - - - +
103E ALA* 4.1 3.1 - - + +
107E LYS 4.8 1.3 - - - +
108E GLY* 1.3 70.5 - - - -
110E TYR* 1.3 63.0 + - - +
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Residues in contact with TYR 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E PHE* 3.4 9.3 - - - +
102E ALA* 2.8 53.0 + - + +
104E THR* 4.2 9.4 - - + +
107E LYS* 3.5 53.4 - - + +
108E GLY 3.4 15.5 - - - -
109E VAL* 1.3 73.5 - - - +
111E LYS* 1.3 69.8 + - - +
112E THR 5.2 0.2 - - - -
124E CYS* 3.7 6.9 - - - +
125E PRO* 2.7 50.3 + - + +
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Residues in contact with LYS 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ARG* 5.2 2.6 - - - +
98E THR* 5.7 0.9 - - - +
99E VAL* 4.0 23.3 - - + +
100E TRP 3.7 4.0 - - - +
101E PHE* 3.7 27.5 - - + -
110E TYR* 1.3 86.5 - - - +
112E THR* 1.3 61.0 + - - +
113E ASN* 5.1 1.4 - - - +
52H ILE* 3.7 28.1 + - - +
53H ASP* 3.9 24.9 + - - +
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Residues in contact with THR 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ILE* 6.0 1.1 - - + -
99E VAL* 3.4 23.7 - - - +
100E TRP* 3.0 41.4 + - + +
101E PHE* 5.2 0.9 - - - -
102E ALA* 5.0 5.1 - - + +
110E TYR* 4.2 3.1 + - - -
111E LYS* 1.3 76.2 - - - +
113E ASN* 1.3 74.1 + - - +
114E THR* 3.8 19.9 + - - +
121E PRO* 4.2 8.8 - - + +
125E PRO* 3.6 34.3 - - + +
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Residues in contact with ASN 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 4.2 6.6 - - - +
111E LYS 5.1 1.0 - - - +
112E THR* 1.3 83.2 + - - +
114E THR* 1.3 61.3 + - - +
115E ALA* 3.5 2.9 + - - +
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Residues in contact with THR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 3.3 7.8 - - - +
100E TRP* 3.2 29.1 + - + +
112E THR* 3.3 9.7 + - - +
113E ASN* 1.3 76.7 - - - +
115E ALA* 1.3 66.5 + - - +
118E SER* 4.2 9.0 - - - -
119E SER 3.5 25.4 - - - +
121E PRO* 3.8 25.1 - - + +
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Residues in contact with ALA 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E THR 4.0 11.0 - - - +
99E VAL* 4.2 4.0 - - + -
100E TRP* 2.9 16.7 + - - -
113E ASN 3.5 3.3 + - - +
114E THR* 1.3 76.3 - - - +
116E VAL* 1.3 64.5 + - - +
117E THR* 3.8 18.2 - - + +
118E SER* 3.2 24.2 + - - +
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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