Contacts of the strand formed by residues 69 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 4.3 19.4 - - + +
67B CYS* 3.7 15.2 + - - +
68B ASP* 1.3 71.8 - - - +
70B TYR* 1.3 66.8 + - - +
71B VAL* 5.3 1.1 - - + -
97B VAL* 3.3 2.6 - - - +
98B LEU* 2.7 33.3 + - - +
99B GLY 3.1 11.0 + - - -
100B GLY 2.8 26.5 + - - -
101B ASN* 4.7 1.7 + - - -
103B PHE* 4.0 20.9 - - + -
148B ALA* 4.5 3.4 - - + -
149B TRP 3.5 8.1 - - - +
163B ILE* 3.9 11.5 - - + +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASP 4.0 0.4 - - - -
69B THR* 1.3 73.9 - - - +
71B VAL* 1.3 74.2 + - - +
72B ARG* 4.0 28.7 + - + -
94B ALA* 5.2 1.6 - - + -
95B THR* 3.5 15.9 - - - +
96B PRO 3.3 26.5 - - - +
97B VAL* 4.0 1.3 - - + +
98B LEU* 4.6 2.0 - - - +
148B ALA* 3.5 5.0 - - - -
149B TRP* 3.0 67.7 + - + +
150B ASP 3.7 7.2 + - - -
151B TRP* 3.6 52.4 - + + -
161B LEU* 6.1 0.3 - - - +
4H FUC 4.2 8.1 - - + -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 5.1 7.4 - - + -
34B LEU* 3.9 32.3 - - + -
37B LEU* 4.8 10.1 - - + -
69B THR* 5.3 2.0 - - + -
70B TYR* 1.3 83.5 - - - +
72B ARG* 1.3 71.1 + - - +
73B VAL* 4.1 11.9 - - + -
94B ALA* 3.2 6.2 - - - +
95B THR* 3.0 43.6 + - + +
98B LEU* 4.8 1.8 - - + -
146B VAL* 4.1 20.4 - - + -
147B GLU 3.2 12.8 - - - +
148B ALA* 4.6 4.7 - - + -
190B LEU* 5.2 1.3 - - + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 4.0 20.4 + - + -
71B VAL* 1.3 79.3 - - - +
73B VAL* 1.3 63.9 + - - +
92B HIS* 4.9 14.6 + - - +
93B GLY 3.6 6.8 + - - -
94B ALA* 3.9 20.7 - - + +
145B ILE 3.8 1.2 - - - +
146B VAL* 3.6 3.8 - - - -
147B GLU* 3.0 39.4 + - - +
149B TRP* 3.8 35.2 - - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 5.1 2.9 - - + -
32B LEU* 4.2 20.2 - - + -
71B VAL* 4.1 11.4 - - + -
72B ARG* 1.3 77.9 - - - +
74B CYS* 1.3 61.9 + - - +
75B LEU* 5.5 0.4 - - + -
88B CYS* 4.9 0.2 - - - -
92B HIS* 3.2 9.7 - - - +
93B GLY 2.8 33.8 + - - +
130B VAL* 3.9 36.3 - - + -
132B ILE* 3.8 19.7 - - + -
144B LEU* 3.7 25.6 - - + -
145B ILE 3.6 2.2 - - - -
146B VAL* 4.9 2.7 - - + +
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Residues in contact with CYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG 4.2 0.2 - - - -
73B VAL* 1.3 75.2 - - - +
75B LEU* 1.3 59.0 + - - +
76B LYS* 4.6 11.9 - - - -
85B THR 4.6 8.5 - - - -
86B GLY* 4.9 1.1 - - - -
87B PRO 4.4 4.5 - - - -
88B CYS* 2.0 54.3 - - - -
91B GLY 4.1 0.7 - - - -
143B THR 3.9 0.6 - - - +
144B LEU* 3.6 6.8 - - - +
145B ILE* 2.9 53.0 + - + +
147B GLU* 6.5 0.7 - - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B PHE* 3.9 49.1 - - + -
74B CYS* 1.3 74.1 - - - +
76B LYS* 1.3 61.6 + - - +
88B CYS* 3.3 3.7 - - - -
89B SER 3.2 7.4 + - - -
90B TYR* 2.9 47.1 + - + +
91B GLY 3.1 17.5 + - - +
132B ILE* 4.6 12.6 - - + -
134B PHE* 5.9 2.0 - - + -
138B TRP* 4.2 12.1 - - + -
142B PHE* 3.7 30.3 - - + -
143B THR 3.7 5.8 - - - +
144B LEU* 4.4 9.6 - - + -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B CYS* 4.6 7.4 - - - -
75B LEU* 1.3 78.0 - - - +
77B GLU* 1.3 74.4 + - - +
79B GLN* 3.6 22.5 - - - +
83B THR* 3.0 25.5 + - - -
85B THR* 2.6 38.4 + - - +
86B GLY 4.8 1.5 + - - -
87B PRO 3.7 24.2 - - - +
88B CYS* 4.3 0.4 - - - -
89B SER 3.7 7.4 - - - +
90B TYR* 3.2 21.6 - - - +
142B PHE* 3.6 0.3 - - - +
143B THR* 2.9 42.8 + - - +
145B ILE* 4.2 9.3 - - + +
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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