Contacts of the strand formed by residues 106 - 116 (chain A) in PDB entry 1X6N
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A LYS 3.8 1.0 + - - -
105A GLY* 1.3 75.3 - - - -
107A ARG* 1.3 64.5 + - - +
108A TYR* 3.7 12.7 - - - -
129A VAL* 3.8 1.0 - - - -
130A VAL* 2.8 34.9 + - - +
136A SER* 3.4 20.9 + - - -
137A HIS* 4.2 2.1 - - - +
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Residues in contact with ARG 107 (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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82A ASN* 4.5 6.1 + - - +
106A GLY* 1.3 74.1 - - - +
108A TYR* 1.3 62.7 + - - +
109A GLN* 5.5 2.3 + - - +
127A GLU* 3.6 26.8 + - - +
128A ILE 3.6 5.2 - - - -
129A VAL* 4.3 15.3 - - + -
136A SER 4.5 2.8 + - - -
137A HIS* 3.0 31.1 + - - +
138A LEU 4.2 2.4 + - - -
139A PRO* 3.9 38.2 - - - +
140A PRO* 5.5 0.4 - - - +
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Residues in contact with TYR 108 (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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81A LEU* 4.0 33.9 - - + -
82A ASN* 3.2 26.2 - - - +
102A VAL* 3.9 11.2 - - + +
104A LYS* 2.6 45.4 + - - +
105A GLY 3.8 5.6 + - - -
106A GLY* 3.7 22.7 - - - -
107A ARG* 1.3 75.3 - - - +
109A GLN* 1.3 64.2 + - - +
110A MET 3.4 2.4 + - - -
127A GLU* 3.2 6.3 - - - +
128A ILE* 2.9 47.8 + - + +
130A VAL* 4.0 19.7 - - + -
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Residues in contact with GLN 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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80A LEU 3.6 1.4 - - - +
81A LEU* 3.7 0.2 - - - -
82A ASN* 2.9 47.5 + - - +
83A GLY 4.7 0.5 + - - -
107A ARG 5.5 1.8 + - - +
108A TYR* 1.3 70.8 - - - +
110A MET* 1.3 60.9 + - - +
111A GLN* 4.1 3.9 + - + +
125A ALA* 3.6 29.5 - - + +
126A THR 4.0 1.3 - - - -
127A GLU* 3.8 31.5 + - - +
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Residues in contact with MET 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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31A ILE* 3.4 27.6 - - + +
36A THR* 6.3 0.2 - - + -
64A VAL* 3.4 44.4 - - + -
79A ILE* 4.0 12.3 - - + -
80A LEU 3.2 10.3 - - - +
81A LEU* 3.8 20.0 - - + -
100A PHE* 5.2 0.4 - - + -
108A TYR 3.4 0.2 + - - -
109A GLN* 1.3 74.3 - - - +
111A GLN* 1.3 78.9 + - - +
112A VAL* 4.5 0.4 - - - -
125A ALA* 3.2 4.2 - - - -
126A THR* 2.8 55.8 + - + +
128A ILE* 4.1 20.4 - - + -
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Residues in contact with GLN 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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79A ILE* 3.4 4.2 - - - -
80A LEU* 2.8 55.9 + - + +
83A GLY* 4.7 9.9 + - - -
109A GLN 4.9 3.9 - - - +
110A MET* 1.3 88.5 - - - +
112A VAL* 1.3 63.4 + - - +
113A ALA 4.1 0.2 - - - -
122A ALA* 3.7 17.2 - - + +
123A SER* 2.9 32.1 + - - +
124A ASP* 4.8 0.6 - - - +
125A ALA* 3.8 20.2 - - + +
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Residues in contact with VAL 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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29A PRO* 3.5 19.0 - - + +
31A ILE* 4.0 13.0 - - + -
64A VAL* 4.0 15.0 - - + -
66A TRP* 3.7 48.2 - - + -
77A ALA* 5.3 0.2 - - + -
78A LYS 3.4 8.1 - - - +
79A ILE* 3.7 20.6 - - + -
110A MET* 4.5 0.2 - - - -
111A GLN* 1.3 75.0 - - - +
113A ALA* 1.3 62.9 + - - +
114A LEU* 4.2 8.5 - - + -
122A ALA* 3.5 1.0 - - - -
123A SER* 2.8 34.4 + - - +
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Residues in contact with ALA 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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76A THR 3.7 0.5 - - - +
77A ALA* 3.4 4.2 - - - +
78A LYS* 2.8 50.4 + - + +
80A LEU* 4.2 21.1 - - + -
112A VAL* 1.3 75.4 - - - +
114A LEU* 1.3 63.8 + - - +
115A CYS* 4.0 11.4 + - - -
120A CYS* 4.8 5.2 - - + -
121A THR 3.4 10.5 - - - +
122A ALA* 4.1 9.0 - - + -
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Residues in contact with LEU 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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26A PRO* 3.3 22.1 - - + +
27A GLY 4.0 6.1 - - - +
29A PRO* 3.8 28.3 - - + -
66A TRP* 4.1 17.5 - - + +
68A LEU* 3.8 26.9 - - + -
72A ASP 4.7 0.2 - - - +
73A ALA* 3.6 19.1 - - + +
76A THR 3.5 2.0 - - - -
77A ALA* 3.9 20.2 - - + -
91A SER* 4.0 11.0 - - - +
112A VAL* 4.2 6.7 - - + -
113A ALA* 1.3 79.8 - - - +
115A CYS* 1.3 60.3 + - - +
121A THR 2.8 31.1 + - - +
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Residues in contact with CYS 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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26A PRO* 3.7 3.1 - - - -
75A THR* 2.8 29.6 + - - -
76A THR* 2.7 31.1 + - - +
78A LYS* 4.1 25.8 - - - -
113A ALA* 4.4 7.9 - - - -
114A LEU* 1.3 76.0 - - - +
116A ASN* 1.3 58.5 + - - +
119A GLY 3.3 5.4 - - - +
120A CYS* 2.0 47.6 - - - -
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Residues in contact with ASN 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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24A ALA 2.9 23.2 + - - -
25A ALA 3.9 0.2 - - - -
26A PRO* 3.5 20.7 - - + +
72A ASP* 5.0 8.7 + - - -
74A GLY* 4.2 3.5 - - - -
75A THR* 3.9 26.7 - - + +
115A CYS* 1.3 76.9 - - - +
117A ALA* 1.3 68.0 + - - +
118A ASP* 2.9 18.5 + - - +
119A GLY* 3.0 26.9 + - - +
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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