Contacts of the strand formed by residues 108 - 118 (chain A) in PDB entry 6N8Q
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 ALA 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS 3.9 0.2 - - - +
104A VAL* 4.1 4.0 - - - +
105A LYS 3.0 30.6 + - - +
106A GLY 3.1 1.8 - - - -
107A GLY* 1.3 78.7 - - - +
109A SER* 1.3 66.4 + - - +
110A GLU* 4.3 2.3 - - + +
428A LEU* 3.8 5.2 - - + -
932A ARG* 3.7 35.7 - - + +
933A CYS 3.3 15.3 - - - +
934A LEU* 4.1 3.6 - - - -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.3 34.8 - - - -
102A LEU* 4.5 5.4 - - - +
103A LYS 3.7 6.5 - - - -
104A VAL* 3.9 12.2 - - - +
108A ALA* 1.3 76.0 - - - +
110A GLU* 1.3 64.3 + - - +
933A CYS* 2.9 14.6 + - - +
934A LEU* 3.6 1.6 - - - +
935A VAL* 2.9 38.0 + - - +
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Residues in contact with GLU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 4.2 2.0 - - - -
101A SER 3.5 0.5 - - - +
102A LEU* 3.4 8.7 - - - -
103A LYS* 3.0 32.4 + - - +
105A LYS* 3.5 36.4 - - - +
108A ALA* 4.3 4.5 - - + +
109A SER* 1.3 80.0 - - - +
111A LEU* 1.3 65.4 + - - +
112A GLN* 3.9 13.6 + - + +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 4.1 12.3 - - + +
58A LEU* 4.0 24.0 - - + -
66A PHE* 3.8 31.9 - - + +
67A MET 3.8 9.9 - - - +
68A GLY* 3.7 31.9 - - - +
88A LEU* 4.8 3.8 - - + -
100A TRP* 3.7 30.5 - - + -
101A SER 3.5 12.1 - - - +
102A LEU* 4.0 5.6 - - + -
110A GLU* 1.3 73.0 - - - +
112A GLN* 1.3 69.1 + - - +
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.3 9.9 - - - -
101A SER* 2.7 51.6 + - - +
103A LYS* 3.5 30.9 - - - +
110A GLU* 3.9 15.6 - - + +
111A LEU* 1.3 79.7 - - - +
113A GLU* 1.3 61.1 + - - +
114A ASP* 3.7 16.0 + - - -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU 4.6 1.2 - - - +
70A HIS* 4.3 9.2 - - - -
71A GLN* 3.9 26.1 + - - +
98A HIS* 2.7 34.5 + - - +
99A LEU 3.8 8.3 - - - +
100A TRP* 3.3 45.3 - - + +
112A GLN* 1.3 73.9 - - - +
114A ASP* 1.3 65.9 + - - +
115A GLU* 3.9 13.2 - - - +
116A SER* 4.1 5.0 - - - -
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLN* 3.4 14.5 - - - +
99A LEU* 2.7 25.0 + - + +
100A TRP 3.7 2.3 - - - -
101A SER* 3.0 34.3 - - - -
112A GLN* 3.7 15.6 + - - +
113A GLU* 1.3 77.6 - - - +
115A GLU* 1.3 76.3 - - - +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A HIS* 3.5 3.1 - - - -
99A LEU* 2.9 47.1 + - + +
113A GLU* 3.8 8.6 - - - +
114A ASP* 1.3 86.6 - - - +
116A SER* 1.3 63.5 + - - +
159A PRO* 2.8 30.0 - - - +
160A ALA* 3.0 23.2 - - - +
161A PHE* 3.4 17.4 - - + +
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLN* 5.8 0.2 + - - -
96A SER* 5.9 1.1 - - - -
97A LEU 3.2 13.7 - - - -
98A HIS* 3.6 22.4 - - - -
113A GLU* 4.1 3.1 - - - -
115A GLU* 1.3 76.9 - - - +
117A PHE* 1.3 65.1 + - - +
161A PHE* 3.6 10.6 - - - +
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A SER* 3.9 0.8 - - - -
97A LEU* 2.9 46.6 + - + +
116A SER* 1.3 79.0 - - - +
118A THR* 1.3 71.3 + - - +
119A LEU* 3.7 30.0 + - + -
120A ARG 5.5 0.4 - - - -
156A VAL* 3.7 24.0 - - + -
161A PHE* 3.3 40.2 - - + -
162A ARG* 4.2 1.1 - - - -
163A ALA* 3.8 39.5 - - + -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP 5.1 5.4 - - - +
95A ASN* 4.4 16.2 - - + +
96A SER* 3.8 15.5 - - - -
117A PHE* 1.3 84.6 - - - +
119A LEU* 1.3 73.1 + - - +
120A ARG* 3.4 10.8 + - + +
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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