Contacts of the strand formed by residues 121 - 130 (chain D) in PDB entry 3AQQ
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 LEU 121 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D ASP 5.5 0.3 - - - +
88D ILE* 3.8 22.0 - - + -
89D PHE* 3.6 20.8 + - - +
111D MET* 3.1 34.3 - - + -
112D CYS 3.2 16.8 - - - +
113D SER* 3.8 15.5 - - - +
114D ILE* 4.2 5.9 - - - +
119D GLU 3.8 7.0 - - - +
120D LYS* 1.3 85.6 - - - +
122D GLN* 1.3 63.9 + - - +
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D PRO* 3.0 46.2 + - - +
49D ARG* 3.0 26.5 + - - +
88D ILE* 3.2 13.1 - - - +
89D PHE* 3.6 22.4 - - + +
90D LEU* 5.0 0.7 - - - +
91D HIS* 4.2 10.9 - - - +
94D ASP* 3.5 7.3 + - - -
111D MET* 3.4 7.3 - - - +
112D CYS* 2.6 43.5 + - + +
113D SER 5.3 0.5 - - - +
114D ILE* 4.0 13.7 - - + +
121D LEU* 1.3 76.2 - - - +
123D ALA* 1.3 75.5 + - - +
124D VAL* 5.1 0.2 - - - -
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Residues in contact with ALA 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ILE* 3.7 29.8 - - + -
88D ILE* 3.7 12.3 - - + -
89D PHE 3.0 10.7 + - - +
90D LEU* 4.4 5.8 - - + +
94D ASP* 3.7 18.7 - - - +
109D TYR* 3.9 14.4 - - + -
110D LYS 3.5 4.3 - - - -
122D GLN* 1.3 78.2 - - - +
124D VAL* 1.3 63.9 + - - +
126D VAL* 3.8 9.5 - - + +
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ARG* 3.5 36.6 - - - +
57D ALA* 3.8 20.4 - - + -
94D ASP* 4.2 7.9 - - - +
109D TYR* 3.7 2.3 - - - -
110D LYS* 2.9 51.3 + - + +
111D MET 4.5 0.4 - - - +
112D CYS* 3.7 21.5 - - + -
122D GLN* 4.9 0.7 - - + -
123D ALA* 1.3 79.3 - - - +
125D GLU* 1.3 80.8 - - + +
126D VAL* 3.4 2.7 - - - -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLU* 5.7 7.8 - - + +
110C LYS* 4.5 1.2 + - - -
125C GLU* 3.5 31.7 - - + +
127C VAL* 4.3 9.0 - - - +
54D THR* 6.1 0.2 - - - +
58D SER* 3.3 29.3 - - - -
94D ASP* 3.8 12.0 + - - +
96D GLU* 4.1 19.7 - - - +
108D THR 3.7 1.0 - - - +
109D TYR* 3.6 11.4 - - - -
110D LYS* 2.9 35.3 + - + +
124D VAL* 1.3 85.0 - - + +
126D VAL* 1.3 60.4 + - - +
127D VAL* 3.7 6.6 + - - +
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ILE* 4.3 12.1 - - + -
90D LEU* 3.8 33.7 - - + -
94D ASP 3.1 16.7 + - - +
95D VAL* 3.9 8.8 - - + +
96D GLU* 3.3 26.7 + - - +
101D PRO* 6.4 0.7 - - + -
107D VAL* 4.4 15.0 - - + -
108D THR 3.5 7.4 - - - +
109D TYR* 3.9 3.1 - - + -
123D ALA* 3.8 20.6 - - + +
124D VAL 3.8 17.9 - - - +
125D GLU* 1.3 71.6 - - - +
127D VAL* 1.3 64.1 + - - +
128D ILE* 4.1 3.7 + - + +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C THR* 4.2 11.2 - - + -
55C VAL* 4.1 21.1 - - + -
58C SER* 3.5 29.6 - - - +
59C GLN* 5.6 0.2 - - - +
125C GLU* 4.3 1.1 - - - +
96D GLU* 3.5 31.2 - - + +
107D VAL* 3.0 8.4 - - - -
108D THR* 2.9 50.4 + - - +
125D GLU 4.2 5.8 - - - +
126D VAL* 1.3 73.4 - - - +
128D ILE* 1.3 73.7 + - - +
129D THR* 3.2 6.3 + - + +
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C PHE* 3.1 37.0 - - + -
55C VAL* 3.4 10.0 - - - +
95D VAL* 5.1 4.7 - - + -
96D GLU 4.8 10.6 + - - +
97D GLY* 6.4 0.2 - - - -
99D TYR* 3.9 34.5 - - + +
101D PRO* 4.3 17.5 - - + -
105D ASP* 4.0 30.1 - - + +
106D GLU 3.5 3.8 - - - +
107D VAL* 4.0 9.9 - - + -
126D VAL* 4.1 5.1 + - + +
127D VAL* 1.3 74.9 - - - +
129D THR* 1.3 57.3 + - - +
130D HIS 3.9 17.9 - - - +
131D LEU* 4.1 5.2 - - + -
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Residues in contact with THR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR* 3.9 9.4 + - - +
111B MET* 5.8 6.3 - - - +
51C PHE* 3.8 11.9 - - - -
55C VAL* 4.3 18.7 - - + +
59C GLN* 5.4 3.4 - - - +
106D GLU* 2.8 19.4 + - - +
107D VAL 4.1 0.9 + - - -
108D THR* 3.4 47.6 - - + +
127D VAL* 3.6 7.2 - - + +
128D ILE* 1.3 73.9 - - - +
130D HIS* 1.3 91.0 + - - -
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Residues in contact with HIS 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B TYR* 3.8 29.8 - + - -
81B PRO* 4.3 16.7 - - + +
82B ALA 4.3 2.2 + - - -
83B ASP* 4.1 35.2 - - + +
84B GLY 4.1 8.3 - - - -
85B GLY* 5.9 0.9 - - - -
86B PRO* 6.6 0.2 - - + -
109B TYR* 5.0 0.8 + - - -
111B MET* 4.4 13.8 - - + +
51C PHE* 4.5 1.8 - - - -
104D GLY 4.5 0.3 - - - +
105D ASP* 3.5 1.9 - - - -
106D GLU* 2.8 55.7 + - + +
128D ILE* 3.4 4.8 - - - +
129D THR* 1.3 112.0 + - - +
131D LEU* 1.3 64.9 + - - +
132D ALA 3.5 0.5 + - - -
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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