Contacts of the strand formed by residues 69 - 76 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.4 15.2 - - + +
39D ASN* 5.7 1.6 - - - +
67D CYS* 3.5 24.0 - - + -
68D ASP* 1.3 71.9 - - - +
70D TYR* 1.3 62.3 + - - +
71D VAL* 5.6 0.5 - - - +
97D VAL* 3.4 1.0 - - - -
98D LEU* 2.9 28.1 + - - +
99D GLY 3.4 6.2 + - - -
100D GLY 3.2 20.8 + - - +
101D ASN* 5.0 1.3 - - - -
103D PHE* 3.2 27.4 - - - -
148D ALA* 5.4 1.8 - - - -
149D TRP 3.2 11.4 - - - -
163D ILE* 3.9 13.5 - - + -
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Residues in contact with TYR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D THR* 1.3 71.9 - - - +
71D VAL* 1.3 77.5 + - - +
72D ARG* 4.0 25.1 + - + -
94D ALA* 5.0 3.1 - - + -
95D THR* 3.4 14.8 - - - +
96D PRO 3.3 27.1 - - - +
97D VAL* 4.1 0.4 - - + +
98D LEU* 4.8 2.0 - - - +
148D ALA* 3.5 1.9 - - - +
149D TRP* 2.9 64.1 + - + +
150D ASP 3.8 12.3 + - - -
151D TRP* 3.6 41.1 - + + -
3J FUC 3.8 15.5 - - + -
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 5.8 2.7 - - + -
34D LEU* 4.0 32.8 - - + -
37D LEU* 4.6 7.9 - - + -
69D THR* 5.6 1.6 - - - +
70D TYR* 1.3 81.0 - - - +
72D ARG* 1.3 65.2 + - - +
73D VAL* 5.0 2.5 - - + -
94D ALA* 3.3 3.5 - - - +
95D THR* 3.0 52.0 + - + +
98D LEU* 4.8 3.6 - - + -
130D VAL* 5.0 7.9 - - + -
146D VAL* 4.6 16.4 - - + -
147D GLU 3.1 13.9 - - - +
148D ALA* 4.3 11.7 - - + -
190D LEU* 6.2 0.9 - - + -
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Residues in contact with ARG 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C GLN* 4.4 18.0 - - - +
70D TYR* 4.0 16.0 - - + -
71D VAL* 1.3 77.9 - - - +
73D VAL* 1.3 66.2 + - - +
93D GLY 3.3 11.1 - - - +
94D ALA* 3.8 17.3 - - + +
145D ILE 3.8 0.7 - - - +
146D VAL* 3.6 3.5 - - - +
147D GLU* 3.0 35.8 + - - +
149D TRP* 3.7 35.6 - - + +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PHE* 5.2 3.1 - - + -
32D LEU* 3.8 27.1 - - + -
71D VAL* 5.0 3.8 - - + -
72D ARG* 1.3 77.7 - - - +
74D CYS* 1.3 65.9 + - - +
75D LEU* 5.4 0.7 - - + -
92D HIS* 3.1 24.8 - - - +
93D GLY 2.8 16.3 + - - +
130D VAL* 4.2 27.4 - - + -
132D ILE* 4.0 22.7 - - + -
144D LEU* 3.6 27.8 - - + -
145D ILE 3.5 2.7 - - - +
146D VAL* 4.7 7.0 - - + -
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Residues in contact with CYS 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 1.3 76.0 - - - +
75D LEU* 1.3 62.0 + - - +
76D LYS* 4.8 8.5 - - - -
86D GLY 5.0 2.5 - - - -
87D PRO 4.9 0.4 - - - -
88D CYS* 2.0 52.7 - - - -
91D GLY 4.1 1.3 - - - -
143D THR 3.6 4.0 - - - +
144D LEU* 3.8 2.8 - - - +
145D ILE* 2.8 61.5 + - + +
147D GLU* 6.4 0.7 - - - -
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D PHE* 3.7 50.3 - - + -
73D VAL* 5.4 0.9 - - + -
74D CYS* 1.3 75.1 - - - +
76D LYS* 1.3 61.7 + - - +
88D CYS* 3.2 10.9 - - - -
90D TYR* 2.8 46.9 + - + +
91D GLY 3.0 18.8 + - - +
132D ILE* 4.6 12.3 - - + -
134D PHE* 5.8 1.8 - - + -
138D TRP* 4.2 10.1 - - + -
142D PHE* 3.9 27.1 - - + -
143D THR 3.7 14.4 - - - +
144D LEU* 4.7 3.8 - - + -
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Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D CYS* 4.8 7.8 - - - -
75D LEU* 1.3 74.8 - - - +
77D GLU* 1.3 70.3 + - - +
79D GLN* 3.4 25.5 + - - +
83D THR* 3.0 43.1 + - - -
85D THR 3.2 12.3 + - - -
86D GLY* 4.9 2.4 + - - -
87D PRO 3.6 16.4 - - - +
88D CYS* 4.2 0.7 - - - -
89D SER* 3.6 22.0 - - - +
90D TYR* 3.2 22.2 - - - +
142D PHE* 3.6 0.5 - - - +
143D THR* 3.0 39.6 + - - +
145D ILE* 4.0 16.5 - - + +
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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