Contacts of the strand formed by residues 108 - 115 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21J ILE* 4.2 20.6 - - - -
22J PRO 5.4 1.3 + - - -
24J LEU* 6.2 1.3 - - - -
70M LYS* 5.5 1.1 - - - -
44N VAL* 5.6 3.1 - - - -
103N ALA* 3.5 0.3 - - - -
104N THR 2.9 36.1 + - - -
105N PRO 3.9 4.5 + - - -
106N ASP 3.5 2.2 - - - -
107N LYS* 1.3 82.0 - - - +
109N VAL* 1.3 61.7 + - - -
110N TYR* 3.4 9.0 - - - -
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Residues in contact with VAL 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ALA* 4.7 8.1 + - + +
18J ALA* 4.6 17.7 - - - +
21J ILE* 4.9 8.9 - - + +
37N THR* 4.3 24.8 - - + +
40N LEU* 3.8 38.4 - - + +
41N ASN* 4.0 10.5 - - + +
44N VAL* 3.9 27.8 - - + -
101N PHE* 4.8 4.5 - - + -
102N ALA 3.6 12.8 - - - +
103N ALA* 4.1 3.1 - - + -
107N LYS 4.8 1.1 - - - +
108N GLY* 1.3 70.7 - - - -
110N TYR* 1.3 63.7 + - - +
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Residues in contact with TYR 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N PHE* 3.4 9.1 - - - +
102N ALA* 2.8 51.8 + - + +
104N THR* 4.2 8.7 - - + +
107N LYS* 3.5 53.8 - - + +
108N GLY 3.4 15.7 - - - -
109N VAL* 1.3 74.6 - - - +
111N LYS* 1.3 70.5 + - - +
112N THR 5.2 0.2 - - - -
124N CYS* 3.7 6.9 - - - +
125N PRO* 2.7 49.9 + - + +
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Residues in contact with LYS 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N ARG* 5.2 9.9 - - - +
98N THR* 5.7 0.7 - - - +
99N VAL* 4.0 23.8 - - + +
100N TRP 3.7 4.3 - - - +
101N PHE* 3.7 28.2 - - + -
110N TYR* 1.3 85.7 - - - +
112N THR* 1.3 60.7 + - - +
113N ASN* 5.1 1.2 - - - +
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Residues in contact with THR 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91N ILE* 6.0 1.8 - - + -
99N VAL* 3.4 23.0 - - - +
100N TRP* 3.0 40.1 + - + +
101N PHE* 4.8 1.1 - - - +
102N ALA* 5.3 4.7 - - + +
110N TYR* 4.2 3.1 + - - -
111N LYS* 1.3 75.5 - - - +
113N ASN* 1.3 74.3 + - - +
114N THR* 3.8 21.2 + - - +
121N PRO* 4.2 8.8 - - + +
125N PRO* 3.6 33.2 - - + +
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Residues in contact with ASN 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N VAL* 4.2 6.6 - - - +
111N LYS 5.1 1.0 - - - +
112N THR* 1.3 82.5 + - - +
114N THR* 1.3 61.0 + - - +
115N ALA* 3.5 2.8 + - - +
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Residues in contact with THR 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N VAL* 3.3 7.5 - - - +
100N TRP* 3.2 28.9 + - + +
112N THR* 3.3 10.1 + - - +
113N ASN* 1.3 77.9 - - - +
115N ALA* 1.3 68.3 + - - +
118N SER* 4.2 8.1 - - - -
119N SER 3.5 24.9 - - - +
121N PRO* 3.8 26.1 - - + +
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Residues in contact with ALA 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N THR 4.0 11.7 - - - +
99N VAL* 4.2 3.8 - - + -
100N TRP* 2.9 16.4 + - - -
113N ASN 3.5 3.7 + - - +
114N THR* 1.3 76.2 - - - +
116N VAL* 1.3 64.0 + - + +
117N THR* 3.3 18.2 - - - +
118N 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