Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 3U8M
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 SER 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.7 0.7 - - - +
51A VAL* 3.8 12.0 - - - +
52A PHE 3.5 3.8 - - - -
53A TRP* 3.5 27.8 + - - -
97A VAL* 3.8 1.0 - - - +
98A LEU* 2.8 45.5 + - - +
99A THR* 2.9 27.8 + - - +
114A MET 3.8 1.2 + - - -
115A PRO* 1.3 72.1 - - - +
117A ILE* 1.3 61.6 + - - +
89E TYR 5.4 3.4 + - - -
143E TRP* 3.8 2.8 - - - -
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Residues in contact with ILE 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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51A VAL* 3.2 4.4 - - - -
52A PHE* 2.7 63.2 + - + +
54A GLN* 3.9 36.1 - - + +
95A PRO* 3.7 30.1 - - + -
96A GLU 3.4 7.4 - - - +
97A VAL* 4.3 12.8 - - + -
98A LEU* 4.3 2.9 - - - -
115A PRO* 4.1 18.8 - - + +
116A SER* 1.3 79.6 + - - +
118A ARG* 1.3 71.0 + - - +
119A GLN* 4.1 3.4 - - + +
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Residues in contact with ARG 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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39A LEU* 3.2 30.6 - - - +
40A GLU* 5.7 2.4 - - - +
49A ASP* 2.9 39.9 + - - +
50A VAL 3.3 6.7 - - - +
51A VAL* 3.7 11.7 - - + -
93A SER* 4.9 0.2 + - - -
94A LYS 4.5 0.9 - - - +
96A GLU* 3.0 53.9 + - - +
98A LEU* 4.1 10.4 - - + +
117A ILE* 1.3 72.9 - - - +
119A GLN* 1.3 66.0 + - - +
47E GLU* 5.5 2.4 + - - -
92E ILE* 2.8 43.1 + - - +
120E ARG* 3.5 27.9 - - - +
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Residues in contact with GLN 119 (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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49A ASP* 4.4 2.0 - - - -
50A VAL 3.0 30.0 + - - +
52A PHE* 3.8 12.0 - - + -
54A GLN* 5.4 0.9 - - - +
88A ALA* 4.2 9.2 - - - +
91A ALA* 3.3 19.5 - - - +
93A SER* 3.0 32.3 + - - +
95A PRO* 3.2 36.7 - - + +
117A ILE* 4.1 6.6 - - + +
118A ARG* 1.3 77.8 - - - +
120A ARG* 1.3 69.1 + - - +
121A PHE* 3.4 31.2 - - + -
98B LEU* 5.4 1.2 + - - +
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Residues in contact with ARG 120 (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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40A GLU* 5.9 2.9 - - - -
47A GLU* 5.3 9.4 + - + -
48A VAL 3.2 8.7 - - - +
49A ASP* 3.5 31.6 - - + +
91A ALA* 3.5 5.4 - - - -
92A ILE* 2.8 44.1 + - + -
93A SER* 3.1 31.4 + - - +
119A GLN* 1.3 75.6 - - - +
121A PHE* 1.3 57.8 + - - +
96B GLU* 5.5 3.0 + - - -
118B ARG* 3.6 33.5 - - - +
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Residues in contact with PHE 121 (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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47A GLU* 3.2 8.5 - - - +
48A VAL* 2.9 45.3 + - + -
50A VAL* 4.4 8.7 - - + -
52A PHE* 3.9 19.7 - + - -
88A ALA* 3.5 27.1 - - + -
90A ASN* 3.4 14.8 - - - +
91A ALA* 3.5 20.0 - - + -
92A ILE* 4.0 6.7 - - - -
119A GLN* 3.4 46.9 - - + -
120A ARG* 1.3 72.1 - - - +
122A SER* 1.3 61.3 + - - +
123A CYS* 3.9 3.7 + - - -
138A ILE* 3.8 40.4 - - + -
140A ILE* 6.3 0.4 - - + -
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Residues in contact with SER 122 (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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46A ASN 3.5 8.1 + - - -
47A GLU* 4.7 2.0 - - - +
90A ASN* 2.9 37.4 + - - +
92A ILE* 3.8 15.1 - - - +
121A PHE* 1.3 69.0 - - - +
123A CYS* 1.3 60.3 + - - +
37B ASN* 2.9 32.5 + - - -
39B LEU* 5.1 2.0 - - - -
166B SER* 3.0 16.1 + - - -
168B TYR* 4.4 8.0 - - - +
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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