Contacts of the strand formed by residues 76 - 83 (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 LEU 76 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D PHE* 3.7 52.5 - - + -
74D VAL* 3.7 16.6 - - + -
75D LEU* 1.3 84.4 - - - +
77D THR* 1.3 63.2 + - - +
97D ILE* 3.1 4.6 - - - +
98D ARG* 2.8 45.6 + - + +
100D PRO* 3.5 31.4 - - + -
114D TRP* 3.9 4.5 - - + -
116D GLU* 4.0 9.2 - - + -
118D ILE* 3.9 4.2 - - - +
137D ASN* 3.6 2.2 - - - -
138D ARG* 4.1 15.3 - - + -
141D TYR* 4.3 6.7 - - + -
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Residues in contact with THR 77 (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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64D PHE* 4.1 2.8 - - - -
76D LEU* 1.3 78.3 - - - +
78D HIS* 1.3 60.8 + - - +
79D THR* 5.0 7.3 + - - -
95D SER* 6.2 0.2 - - - -
96D ALA 3.4 6.3 - - - -
97D ILE* 3.8 14.4 - - + -
118D ILE* 4.9 0.2 - - - -
136D ILE* 3.2 25.3 - - - +
137D ASN* 2.9 36.4 + - - +
106W LEU* 3.8 37.2 - - + +
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Residues in contact with HIS 78 (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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28D TRP* 5.5 0.4 - + - -
60D SER* 3.1 38.4 + - - -
62D VAL* 3.4 44.2 - - + +
76D LEU 4.3 0.2 + - - -
77D THR* 1.3 75.1 - - - +
79D THR* 1.3 67.8 + - - +
96D ALA 2.9 30.9 + - - -
118D ILE* 3.8 29.4 - - + +
120D LEU* 3.4 25.5 - - + +
134D ALA* 4.3 16.6 - - + -
135D GLU 3.2 16.0 + - - -
136D ILE* 3.6 6.5 - - + +
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Residues in contact with THR 79 (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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77D THR* 5.0 7.3 + - - -
78D HIS* 1.3 83.3 + - - +
80D ILE* 1.3 69.2 + - - +
81D SER* 3.6 5.4 + - - +
92D ASN* 3.6 33.4 + - + +
94D LEU 3.4 11.0 - - - +
95D SER* 3.3 14.4 + - - -
120D LEU* 4.0 0.7 - - - -
133D SER 3.4 3.5 - - - +
134D ALA* 4.4 0.2 - - - -
135D GLU* 2.8 41.2 + - - +
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Residues in contact with ILE 80 (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* 3.7 27.6 - - + -
59D TYR 3.8 5.8 - - - -
60D SER* 3.4 33.4 - - - +
78D HIS* 5.0 0.2 - - + -
79D THR* 1.3 71.4 - - - +
81D SER* 1.3 68.1 + - - +
92D ASN 4.0 0.2 - - - -
93D LEU* 3.0 29.2 + - + +
94D LEU* 2.8 38.3 + - + +
120D LEU* 3.8 7.7 - - + +
132D LEU* 4.8 6.3 - - + -
133D SER 3.4 6.1 - - - +
134D ALA* 3.9 13.2 - - + -
152D PHE* 3.7 18.4 - - + -
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Residues in contact with SER 81 (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 5.9 + - - -
80D ILE* 1.3 74.6 - - - +
82D ARG* 1.3 62.1 + - - +
83D ILE* 4.9 2.6 - - - +
90D PRO* 3.8 18.2 - - - +
91D VAL 3.2 21.8 - - - -
92D ASN* 4.0 11.7 - - - -
93D LEU* 4.5 2.2 - - - -
131D ARG 3.9 0.2 - - - +
132D LEU* 3.4 9.1 - - - +
133D SER* 2.8 46.8 + - - -
135D GLU* 5.7 0.6 - - - -
109W GLN* 5.6 1.1 - - - -
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Residues in contact with ARG 82 (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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81D SER* 1.3 74.0 - - - +
83D ILE* 1.3 65.8 + - - +
84D ALA* 3.5 25.7 + - - +
86D SER* 4.7 4.9 + - - -
89D THR 3.1 5.4 - - - +
91D VAL* 2.7 40.8 + - + +
93D LEU* 3.4 25.6 - - + -
125D GLN 3.9 16.3 + - - -
126D LEU* 3.4 20.0 - - + +
127D GLU* 4.0 11.3 - - - +
130D ASP* 2.6 35.0 + - + -
131D ARG 3.6 5.2 - - - +
132D LEU* 4.1 10.8 - - + -
34F ASN* 2.8 39.2 + - - +
68W VAL* 6.3 1.0 - - - +
69W PRO* 6.3 1.2 - - - +
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Residues in contact with ILE 83 (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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47D GLN* 4.4 15.9 - - - +
81D SER* 4.9 3.6 - - - +
82D ARG* 1.3 76.5 - - - +
84D ALA* 1.3 67.5 + - - +
85D VAL* 3.7 0.5 + - - +
88D GLN* 4.1 11.2 - - + -
89D THR* 3.6 23.3 - - - +
90D PRO* 3.9 26.5 - - + -
129D GLY 4.6 1.2 - - - +
130D ASP* 3.9 0.9 - - - -
131D ARG* 2.9 71.9 + - + +
133D SER* 5.7 3.8 - - - +
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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