Contacts of the strand formed by residues 69 - 76 (chain C) in PDB entry 5MWF
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 THR 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LEU* 4.2 21.0 - - + +
67C CYS* 3.3 15.1 + - - +
68C ASP* 1.3 71.4 - - - +
70C TYR* 1.3 68.6 + - - +
71C VAL* 5.4 0.7 - - + -
97C VAL* 3.3 3.3 - - - -
98C LEU* 3.0 28.2 + - - +
99C GLY 3.5 5.8 + - - -
100C GLY 2.7 26.9 + - - -
101C ASN 4.8 1.7 + - - -
103C PHE* 3.9 23.6 - - + -
148C ALA* 4.3 4.3 - - + -
149C TRP 3.3 5.6 - - - -
163C ILE* 3.9 16.3 - - + +
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Residues in contact with TYR 70 (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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68C ASP 3.7 0.9 - - - -
69C THR* 1.3 73.4 - - - +
71C VAL* 1.3 72.0 + - - +
72C ARG* 4.5 15.3 - - + -
94C ALA* 5.5 2.0 - - + -
95C THR* 3.5 8.3 - - - +
96C PRO 3.1 26.0 - - - +
97C VAL* 4.1 0.9 - - - -
98C LEU* 4.1 2.9 - - - -
148C ALA* 3.4 4.3 - - - -
149C TRP* 2.9 84.8 + + + +
150C ASP 3.8 3.4 + - - -
151C TRP* 3.5 56.9 - + + -
161C LEU* 5.9 1.4 - - - +
4I FUC 3.6 17.0 - - + -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 5.7 4.3 - - + -
34C LEU* 3.7 31.0 - - + -
37C LEU* 5.1 11.2 - - + -
69C THR* 5.4 0.9 - - + -
70C TYR* 1.3 80.4 - - - +
72C ARG* 1.3 72.4 + - - +
73C VAL* 4.4 8.1 - - + -
94C ALA* 3.3 4.2 - - - +
95C THR* 2.9 49.2 + - + +
98C LEU* 4.1 6.5 - - + -
103C PHE* 5.3 1.8 - - + -
130C VAL* 6.0 0.2 - - + -
146C VAL* 3.7 23.8 - - + -
147C GLU 3.4 11.7 - - - +
148C ALA* 5.3 1.6 - - + -
190C LEU* 5.6 2.9 - - + -
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Residues in contact with ARG 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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70C TYR* 4.5 14.1 - - + -
71C VAL* 1.3 78.8 - - - +
73C VAL* 1.3 64.3 + - - +
92C HIS* 5.7 4.8 + - - +
93C GLY 3.5 8.0 + - - +
94C ALA* 4.1 15.6 - - + +
145C ILE 3.9 0.5 - - - +
146C VAL* 3.5 4.9 - - - +
147C GLU* 2.4 77.6 + - + +
149C TRP* 4.0 26.0 - - + +
135D GLN* 2.8 43.4 + - - +
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Residues in contact with VAL 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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30C PHE* 5.1 3.8 - - + -
32C LEU* 4.0 33.7 - - + -
71C VAL* 4.4 11.2 - - + -
72C ARG* 1.3 80.2 - - - +
74C CYS* 1.3 64.7 + - - +
75C LEU* 5.3 0.2 - - + -
92C HIS* 3.2 9.0 - - - +
93C GLY 3.0 32.5 + - - +
130C VAL* 4.4 20.9 - - + -
132C ILE* 4.0 18.8 - - + -
144C LEU* 3.6 24.2 - - + -
145C ILE 3.5 2.2 - - - -
146C VAL* 4.5 5.2 - - + -
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Residues in contact with CYS 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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73C VAL* 1.3 75.5 - - - +
75C LEU* 1.3 59.3 + - - +
76C LYS* 4.2 15.1 - - - +
86C GLY 4.9 2.2 - - - -
87C PRO 4.8 0.2 - - - -
88C CYS* 2.0 54.3 - - - -
91C GLY 4.0 1.6 - - - -
143C THR 3.8 1.2 - - - +
144C LEU* 3.7 4.2 - - - +
145C ILE* 2.8 57.9 + - + +
147C GLU* 5.9 4.5 - - - +
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Residues in contact with LEU 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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30C PHE* 3.6 50.9 - - + -
73C VAL 4.3 0.2 - - - -
74C CYS* 1.3 73.4 - - - +
76C LYS* 1.3 57.4 + - - +
88C CYS* 3.2 10.5 - - - -
90C TYR* 2.8 48.2 + - + +
91C GLY 3.1 15.9 + - - +
132C ILE* 4.4 17.7 - - + -
134C PHE* 6.1 0.9 - - + -
138C TRP* 4.0 9.6 - - + -
142C PHE* 3.6 35.9 - - + -
143C THR 3.6 7.6 - - - +
144C LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 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 CYS* 4.7 8.7 - - - +
75C LEU* 1.3 76.3 - - - +
77C GLU* 1.3 74.3 - - - +
79C GLN* 3.2 29.4 - - - +
83C THR 3.2 19.7 + - - -
85C THR 3.3 20.6 + - - -
86C GLY* 4.7 2.6 - - - +
87C PRO* 3.6 16.2 - - + +
88C CYS* 4.1 0.9 - - - -
89C SER 3.5 19.7 - - - +
90C TYR* 3.2 21.2 - - - +
142C PHE* 3.7 0.3 - - - +
143C THR* 3.0 39.9 + - - +
145C ILE* 3.9 21.5 - - - +
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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