Contacts of the strand formed by residues 116 - 122 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B TYR 5.4 3.7 + - - -
143B TRP* 3.9 3.1 - - - -
36C ILE* 4.7 0.9 - - - +
51C VAL* 3.8 11.8 - - - +
52C PHE 3.5 4.3 - - - -
53C TRP* 3.5 28.4 + - - -
97C VAL* 3.8 1.0 - - - +
98C LEU* 2.8 45.4 + - - +
99C THR* 3.0 28.2 + - - +
114C MET 3.9 0.6 + - - -
115C PRO* 1.3 71.7 - - - +
117C ILE* 1.3 61.8 + - - +
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 3.1 4.5 - - - -
52C PHE* 2.7 62.4 + - + +
54C GLN* 3.8 38.1 - - + +
95C PRO* 3.7 28.0 - - + -
96C GLU 3.4 7.0 - - - +
97C VAL* 4.4 11.0 - - + -
98C LEU* 4.4 3.1 - - - -
115C PRO* 4.1 18.8 - - + +
116C SER* 1.3 81.3 + - - +
118C ARG* 1.3 74.8 + - - +
119C GLN* 4.1 2.9 - - + +
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Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLU* 5.5 1.6 + - - -
92B ILE* 2.9 32.2 + - - +
120B ARG* 3.5 32.5 - - - +
39C LEU* 3.2 31.1 - - - +
40C GLU* 5.8 1.6 - - - +
49C ASP* 2.9 40.2 + - - +
50C VAL 3.2 7.0 - - - +
51C VAL* 3.6 9.9 - - + -
93C SER* 5.0 0.2 + - - -
94C LYS 4.5 0.5 - - - +
96C GLU* 2.9 54.1 + - - +
98C LEU* 4.1 10.1 - - + +
117C ILE* 1.3 73.0 - - - +
119C GLN* 1.3 64.4 + - - +
120C ARG* 5.9 1.1 - - + +
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Residues in contact with GLN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP* 4.4 0.9 - - - -
50C VAL 2.9 30.0 + - - +
52C PHE* 3.9 12.7 - - + -
54C GLN* 5.4 1.0 - - - +
88C ALA* 4.3 9.6 - - - +
91C ALA* 3.2 20.4 - - + +
93C SER* 3.0 32.0 + - - +
95C PRO* 3.3 33.9 - - + +
117C ILE* 4.1 7.2 - - + +
118C ARG* 1.3 76.2 - - - +
120C ARG* 1.3 73.2 + - - +
121C PHE* 3.5 28.1 - - + -
98D LEU 5.2 2.2 + - - -
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Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C GLU* 6.1 0.2 - - - -
47C GLU* 6.0 1.1 - - + -
48C VAL 3.2 7.0 - - - +
49C ASP* 3.3 37.7 + - + +
91C ALA* 3.4 7.1 - - - +
92C ILE* 2.8 44.5 + - + -
93C SER* 3.1 39.7 + - - +
118C ARG* 5.9 1.2 - - + +
119C GLN* 1.3 74.1 - - - +
121C PHE* 1.3 57.8 + - - +
96D GLU* 5.3 1.6 + - - -
118D ARG* 4.2 17.6 - - - +
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Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU* 3.1 8.5 - - - +
48C VAL* 2.9 48.8 + - + +
50C VAL* 4.4 6.7 - - + -
52C PHE* 3.9 21.1 - + - -
88C ALA* 3.6 26.7 - - + -
90C ASN* 3.4 19.3 - - - +
91C ALA* 3.6 21.5 - - + -
92C ILE* 4.1 5.6 - - - -
119C GLN* 3.5 41.3 - - + -
120C ARG* 1.3 75.5 - - - +
122C SER* 1.3 60.2 + - - +
123C CYS* 3.9 4.6 + - - -
138C ILE* 3.9 34.8 - - + -
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASN 3.5 8.7 + - - -
47C GLU* 4.7 3.6 - - - +
90C ASN* 2.9 37.2 + - - +
92C ILE* 3.9 14.2 - - - +
121C PHE* 1.3 69.6 - - - +
123C CYS* 1.3 62.1 + - - +
37D ASN* 2.9 32.1 + - - -
39D LEU* 5.2 0.2 - - - -
166D SER* 3.2 15.8 + - - -
168D TYR* 4.2 10.6 - - - +
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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