Contacts of the strand formed by residues 71 - 78 (chain C) in PDB entry 2UYK
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 ILE 71 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS* 4.7 4.3 + - - -
57C VAL* 4.2 22.0 - - + -
58C LYS* 5.5 2.0 - - - -
61C VAL* 4.2 21.1 - - + -
67C SER 4.3 2.9 - - - +
68C VAL* 3.0 35.1 + - + +
69C GLY 4.3 5.2 - - - +
70C ASP* 1.3 79.0 - - - +
72C ILE* 1.3 62.3 + - - +
73C LYS 3.9 12.1 - - - +
74C MET* 3.9 12.8 - - + -
94C PHE* 5.1 3.8 - - + -
95C PHE* 4.3 15.7 - - + -
101C THR 4.8 2.4 - - - +
103C PRO* 3.5 30.9 - - + +
123C ALA* 4.2 4.3 - - + -
124C ILE 3.7 11.4 - - - +
125C ALA* 3.9 4.5 - - + -
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Residues in contact with ILE 72 (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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2A LYS* 4.1 16.6 - - + -
21A VAL* 4.0 29.4 - - + +
23A LEU* 4.1 9.4 - - + -
28A PHE* 4.0 30.2 - - + +
70C ASP 3.6 9.6 - - - +
71C ILE* 1.3 78.6 - - - +
73C LYS* 1.3 71.3 + - + +
103C PRO* 3.4 8.5 - - - +
104C THR* 2.9 28.4 + - - +
124C ILE* 2.9 27.6 + - + +
126C VAL* 3.7 32.8 - - + -
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Residues in contact with LYS 73 (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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28A PHE* 4.2 19.7 - - + -
29A THR 4.0 15.5 - - - +
122A GLU* 2.9 27.5 + - - -
71C ILE* 3.9 0.9 - - - +
72C ILE* 1.3 91.8 - - + +
74C MET* 1.3 81.4 + - - +
75C THR* 2.9 27.9 + - - -
103C PRO* 3.7 1.0 - - - +
104C THR* 3.0 27.6 - - - +
105C ARG 4.5 0.4 - - - -
106C SER* 3.7 10.1 + - - +
122C GLU* 5.1 0.2 + - - -
123C ALA* 3.3 3.3 - - - -
124C ILE* 2.9 44.9 + - + +
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Residues in contact with MET 74 (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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54C LEU* 4.3 7.0 - - + -
57C VAL* 4.0 12.3 - - + -
71C ILE* 3.9 10.5 - - + -
73C LYS* 1.3 92.9 + - - +
75C THR* 1.3 64.8 + - - +
76C VAL 4.2 0.2 - - - -
91C TYR* 3.2 43.7 - - + +
94C PHE* 6.2 0.2 - - + -
95C PHE* 3.7 15.9 - - + -
103C PRO* 3.7 10.8 - - + -
104C THR 2.9 5.8 + - - +
105C ARG* 3.2 7.6 - - + -
106C SER 3.2 13.7 + - - -
121C ILE* 3.7 23.3 - - + -
122C GLU* 3.2 7.2 - - - +
123C ALA* 3.6 26.9 - - + +
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Residues in contact with THR 75 (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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77A PHE* 4.9 8.3 - - + -
122A GLU* 4.2 3.5 + - - +
73C LYS* 2.9 21.0 + - - -
74C MET* 1.3 73.0 - - - +
76C VAL* 1.3 63.6 + - - +
77C PHE* 3.5 34.1 - - + -
106C SER* 3.4 20.4 - - - +
107C CYS* 5.4 0.7 - - - -
108C VAL* 5.5 1.3 - - + -
120C GLU 3.7 1.6 - - - +
121C ILE* 3.3 6.6 - - - +
122C GLU* 3.0 57.9 + - - +
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Residues in contact with VAL 76 (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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74C MET* 4.7 1.1 - - + -
75C THR* 1.3 78.5 - - - +
77C PHE* 1.3 60.8 + - - +
78C ILE* 3.6 22.9 - - + -
84C PHE* 5.7 1.1 - - + -
87C ILE* 4.5 10.8 - - + -
91C TYR* 3.8 30.3 - - + -
105C ARG* 3.9 15.9 - - + +
106C SER 2.9 9.6 + - - +
107C CYS* 3.2 33.3 - - + -
108C VAL 3.2 5.5 + - - -
119C LEU* 4.5 10.3 - - + -
120C GLU 3.7 2.2 - - - -
121C ILE* 4.1 23.6 - - + -
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Residues in contact with PHE 77 (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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77A PHE* 4.5 13.9 - + - -
75B THR* 5.1 4.7 - - + -
77B PHE* 4.7 9.0 - + - -
106B SER* 4.5 12.8 - - - -
108B VAL* 3.7 40.8 - - + -
75C THR* 3.5 32.3 - - + -
76C VAL* 1.3 71.8 - - - +
78C ILE* 1.3 60.0 + - - +
108C VAL* 3.6 26.9 - - + -
110C VAL* 3.9 10.3 - - + -
113C LEU* 3.7 11.4 - - + +
119C LEU* 3.1 6.8 - - - +
120C GLU* 2.8 50.8 + - + +
122C GLU* 4.4 18.4 - - + -
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Residues in contact with ILE 78 (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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76C VAL* 3.6 23.1 - - + -
77C PHE* 1.3 79.3 - - - +
79C THR* 1.3 63.9 + - - +
80C ASP 3.7 22.4 - - - +
81C LEU* 3.9 30.3 - - + -
83C ASP* 5.9 0.2 - - + -
84C PHE* 4.2 16.6 - - + -
87C ILE* 3.7 23.6 - - + -
107C CYS* 4.3 7.6 - - - -
108C VAL 3.0 15.7 + - - +
109C GLN* 3.1 10.5 - - + -
110C VAL* 2.8 27.8 + - - +
113C LEU* 4.5 0.2 - - - -
118C LYS 3.3 9.2 - - - +
119C LEU* 4.1 3.1 - - + +
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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