Contacts of the strand formed by residues 89 - 95 (chain C) in PDB entry 3UDB
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 HIS 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C PRO* 2.4 39.5 - - + +
51C TYR* 4.4 11.3 + + + +
52C ILE 2.5 32.6 - - - +
53C GLU* 3.3 27.1 + - + +
54C ARG* 3.5 15.3 - - - -
85C LEU* 3.9 0.6 - - - -
86C THR* 2.9 38.0 + - - +
88C THR* 1.3 117.9 + - + +
90C LEU* 1.3 59.1 + - - +
91C ALA 3.7 0.2 + - - -
315C ALA* 5.3 0.7 - - - -
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Residues in contact with LEU 90 (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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50C LYS 3.8 0.5 - - - +
51C TYR* 3.5 6.2 - - - -
52C ILE* 2.8 36.8 + - + +
54C ARG* 4.6 2.0 - - - +
58C ILE* 3.6 29.8 - - + -
62C VAL* 4.6 11.2 - - + -
66C ILE* 3.9 25.4 - - + -
83C VAL* 4.0 17.3 - - + -
84C ILE 3.8 10.5 - - - +
85C LEU* 4.7 2.0 - - + +
89C HIS* 1.3 72.3 - - - +
91C ALA* 1.3 67.4 + - - +
92C ILE* 4.0 9.0 + - + +
311C ILE* 4.1 25.1 - - + +
312C ILE* 4.6 10.5 - - + -
315C ALA* 4.2 5.6 - - + -
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Residues in contact with ALA 91 (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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16C HIS* 4.2 7.9 - - - +
49C VAL* 4.0 10.5 - - + -
50C LYS 3.5 4.9 - - - -
51C TYR* 3.8 24.2 - - + -
83C VAL* 3.3 8.1 - - - +
84C ILE* 2.7 55.9 + - + +
86C THR* 4.8 3.4 - - + -
89C HIS 3.7 1.4 + - - -
90C LEU* 1.3 72.7 - - - +
92C ILE* 1.3 60.6 + - - +
93C VAL* 3.9 2.4 + - + +
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Residues in contact with ILE 92 (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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48C ALA 3.7 1.2 - - - +
49C VAL* 3.3 2.6 - - - -
50C LYS* 2.8 51.6 + - + +
52C ILE* 3.8 31.2 - - + -
62C VAL* 5.1 0.2 - - + -
66C ILE* 4.1 25.4 - - + -
69C HIS* 5.8 2.2 - - - +
80C PHE* 4.2 23.8 - - + -
82C GLU 4.2 1.8 - - - -
83C VAL* 4.2 12.1 - - + -
90C LEU* 4.4 6.3 - - + +
91C ALA* 1.3 76.6 - - - +
93C VAL* 1.3 61.3 + - - +
94C MET* 3.9 20.7 - - + +
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Residues in contact with VAL 93 (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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16C HIS* 6.2 0.2 - - - +
21C TYR* 4.2 17.0 - - + +
38C MET* 6.1 0.2 - - - -
47C VAL* 3.3 38.1 - - + -
48C ALA 3.5 2.9 - - - -
49C VAL* 4.0 18.8 - - + -
80C PHE* 4.1 4.2 - - - -
81C LYS* 3.1 30.0 + - + +
82C GLU* 3.0 25.7 + - + +
84C ILE* 4.3 25.8 - - + -
91C ALA* 4.6 3.1 - - + +
92C ILE* 1.3 75.4 - - - +
94C MET* 1.3 62.3 + - - +
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Residues in contact with MET 94 (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 VAL* 3.6 6.0 - - - +
48C ALA* 2.9 36.8 + - + +
50C LYS* 4.3 17.7 - - + +
69C HIS* 4.1 23.8 - - + +
78C VAL* 4.6 8.5 - - + -
79C ARG 3.5 15.5 - - - +
80C PHE* 4.4 1.6 - - + -
81C LYS* 4.3 7.9 - - - -
92C ILE* 3.9 35.9 - - + +
93C VAL* 1.3 77.1 - - - +
95C GLU* 1.3 74.1 + - - +
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Residues in contact with GLU 95 (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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45C GLU* 5.0 6.2 - - - +
46C LEU 4.8 1.3 - - - -
47C VAL* 4.8 2.5 - - - -
48C ALA* 4.6 1.6 - - - +
77C ILE 3.3 2.6 - - - +
78C VAL* 3.6 16.3 - - + +
79C ARG* 2.9 69.4 + - + +
81C LYS* 3.9 27.0 + - - +
94C MET* 1.3 88.2 - - - +
96C TYR* 1.3 61.6 + - - +
97C ALA 4.2 0.6 + - - -
157C LYS* 2.9 26.2 + - + +
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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