Contacts of the strand formed by residues 91 - 98 (chain D) in PDB entry 3ALQ
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 VAL 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D SER* 3.8 1.1 - - - -
82D ARG* 2.7 41.1 + - + +
87D TYR* 3.9 27.8 - - + -
89D THR 3.5 11.0 - - - +
90D PRO* 1.3 80.6 - - - +
92D ASN* 1.3 73.5 + - - +
93D LEU* 3.1 5.2 + - - +
34F ASN* 3.8 24.9 - - - +
147F SER* 5.0 5.2 - - - +
72W LEU* 4.5 17.9 - - + -
109W GLN* 6.1 0.2 - - - -
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Residues in contact with ASN 92 (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 THR* 3.6 27.5 + - + +
80D ILE 4.0 5.2 - - - -
81D SER* 4.0 6.2 - - - +
91D VAL* 1.3 75.9 - - - +
93D LEU* 1.3 65.2 + - - +
95D SER* 4.2 9.5 + - - -
34F ASN* 6.0 0.2 - - - +
146F GLU* 2.9 35.6 + - - -
147F SER* 3.2 44.5 + - - +
148F GLY 4.1 0.2 + - - -
109W GLN* 4.1 20.6 - - - +
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Residues in contact with LEU 93 (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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58D ILE* 4.3 5.8 - - + -
80D ILE* 3.0 12.3 + - + +
81D SER 4.7 0.4 - - - -
82D ARG* 3.4 38.1 - - + +
91D VAL 3.7 8.1 - - - +
92D ASN* 1.3 76.7 - - - +
94D LEU* 1.3 70.4 + - + +
124D PHE* 3.4 40.1 - - + -
126D LEU* 4.8 0.2 - - + -
132D LEU* 3.9 16.6 - - + -
15F HIS* 4.8 2.6 + - - -
34F ASN* 3.3 42.8 - - + +
148F GLY* 3.3 15.7 - - - -
151F TYR* 4.6 1.9 - - - -
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Residues in contact with LEU 94 (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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58D ILE* 3.5 27.1 - - + +
79D THR* 3.4 3.5 - - - +
80D ILE* 2.8 55.9 + - + +
93D LEU* 1.3 88.0 - - + +
95D SER* 1.3 63.4 + - - +
120D LEU* 3.5 19.3 - - + -
121D GLY* 3.6 17.0 - - - +
122D GLY* 3.9 1.6 - - - +
124D PHE* 3.8 21.3 - - + -
148F GLY 3.7 2.7 - - - -
151F TYR* 3.3 38.4 - - + +
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Residues in contact with SER 95 (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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78D HIS 3.5 6.7 - - - -
79D THR* 3.3 14.2 + - - -
92D ASN* 4.2 11.4 + - - -
94D LEU* 1.3 76.0 - - - +
96D ALA* 1.3 64.9 + - - +
97D ILE* 5.4 2.4 - - - +
120D LEU* 3.9 4.6 - - - +
61F GLN* 2.8 23.8 + - - -
146F GLU* 5.1 1.4 + - - +
147F SER 3.7 20.4 - - - -
148F GLY 2.9 9.4 + - - +
149F GLN* 3.6 24.1 + - - +
113W ARG* 5.4 1.0 + - - -
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Residues in contact with ALA 96 (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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76D LEU 3.9 0.2 - - - +
77D THR* 3.4 3.3 - - - -
78D HIS 2.9 32.4 + - - -
79D THR* 5.0 0.2 + - - -
95D SER* 1.3 81.3 + - - +
97D ILE* 1.3 66.2 + - - +
118D ILE* 3.8 16.9 - - + +
119D TYR 5.4 0.2 - - - +
120D LEU* 3.7 18.4 - - + -
61F GLN* 4.2 4.7 - - - +
63F LEU* 4.5 7.9 - - + -
117F PRO* 4.1 21.5 - - + -
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Residues in contact with ILE 97 (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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75D LEU* 4.5 2.0 - - + -
76D LEU 3.1 16.8 - - - +
77D THR* 3.8 16.8 - - + -
95D SER* 5.4 2.9 - - - +
96D ALA* 1.3 80.6 - - - +
98D ARG* 1.3 75.1 + - - +
118D ILE* 4.2 0.9 - - - -
63F LEU* 3.8 8.2 - - + +
115F TYR* 3.6 38.6 - - + +
117F PRO* 3.0 25.4 - - - +
149F GLN* 5.4 0.7 - - - +
106W LEU* 3.8 17.3 - - + -
113W ARG* 3.1 50.9 - - - +
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Residues in contact with ARG 98 (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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75D LEU* 3.7 1.0 - - - -
76D LEU* 2.8 37.1 + - + +
97D ILE* 1.3 77.7 - - - +
99D SER* 1.3 98.5 + - - +
100D PRO* 4.3 1.9 - - - +
102D GLN* 5.7 0.8 - - - +
116D GLU* 3.0 42.7 + - + +
117D PRO 4.7 4.0 - - - +
118D ILE* 3.7 23.6 - - + -
98E ARG* 2.9 28.3 - - - +
98F ARG* 3.3 14.8 - - - +
114F TRP* 5.9 0.2 - - - +
115F TYR* 3.1 22.9 + - - +
116F GLU* 3.3 19.4 + - - -
117F PRO* 3.7 17.3 - - - -
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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